rs61754381

Variant names:

• chr11-89227816-T-A
• rs61754381
• NM_000372.5:c.1037-7T>A

Your query was ambiguous. Multiple possible variants found:

• chr11-89227816-T-A
• chr11-89227816-T-C

Variant summary

Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PP3 PP5_Very_Strong

The NM_000372.5(TYR):​c.1037-7T>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000504 in 1,611,808 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.00050 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00050 (3 hom.)
• Consequence: TYR NM_000372.5 splice_region, intron
• Scores: Splicing: ADA: 0.9983
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:36 O:1
• Conservation: PhyloP100: -0.500

Genes affected

TYR (HGNC:12442): (tyrosinase) The enzyme encoded by this gene catalyzes the first 2 steps, and at least 1 subsequent step, in the conversion of tyrosine to melanin. The enzyme has both tyrosine hydroxylase and dopa oxidase catalytic activities, and requires copper for function. Mutations in this gene result in oculocutaneous albinism, and nonpathologic polymorphisms result in skin pigmentation variation. The human genome contains a pseudogene similar to the 3' half of this gene. [provided by RefSeq, Oct 2008]

ACMG classification

Verdict is Likely_pathogenic. Variant got 9 ACMG points.

• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 11-89227816-T-A is Pathogenic according to our data. Variant chr11-89227816-T-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 99527.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-89227816-T-A is described in Lovd as [Pathogenic]. Variant chr11-89227816-T-A is described in Lovd as [Likely_pathogenic]. Variant chr11-89227816-T-A is described in Lovd as [Pathogenic]. Variant chr11-89227816-T-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TYR	NM_000372.5	c.1037-7T>A		splice_region_variant, intron_variant	Intron 2 of 4	ENST00000263321.6	NP_000363.1
TYR	XM_011542970.3	c.1037-7T>A		splice_region_variant, intron_variant	Intron 2 of 5		XP_011541272.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TYR	ENST00000263321.6	c.1037-7T>A		splice_region_variant, intron_variant	Intron 2 of 4	1	NM_000372.5	ENSP00000263321.4

Frequencies

GnomAD3 genomes AF: 0.000493 AC: 75 AN: 152184 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000724

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000328

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0000941

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000309

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000950 AC: 237 AN: 249548 Hom.: 1 AF XY: 0.000963 AC XY: 130 AN XY: 134970

Gnomad AFR exome AF: 0.0000616

Gnomad AMR exome AF: 0.000437

Gnomad ASJ exome AF: 0.0152

Gnomad EAS exome AF: 0.000273

Gnomad SAS exome AF: 0.0000655

Gnomad FIN exome AF: 0.0000480

Gnomad NFE exome AF: 0.000380

Gnomad OTH exome AF: 0.00280

GnomAD4 exome AF: 0.000505 AC: 737 AN: 1459506 Hom.: 3 Cov.: 32 AF XY: 0.000545 AC XY: 396 AN XY: 726144

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000404

Gnomad4 ASJ exome AF: 0.0152

Gnomad4 EAS exome AF: 0.000353

Gnomad4 SAS exome AF: 0.000151

Gnomad4 FIN exome AF: 0.0000191

Gnomad4 NFE exome AF: 0.000179

Gnomad4 OTH exome AF: 0.00146

GnomAD4 genome AF: 0.000499 AC: 76 AN: 152302 Hom.: 0 Cov.: 32 AF XY: 0.000510 AC XY: 38 AN XY: 74472

Gnomad4 AFR AF: 0.0000722

Gnomad4 AMR AF: 0.000327

Gnomad4 ASJ AF: 0.0127

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.0000941

Gnomad4 NFE AF: 0.000309

Gnomad4 OTH AF: 0.00

Alfa AF: 0.00209 Hom.: 1

Bravo AF: 0.000484

EpiCase AF: 0.000874

EpiControl AF: 0.000534

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:36 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:8 Other:1

-

Clinical Genetics, Academic Medical Center

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jul 01, 2021

CeGaT Center for Human Genetics Tuebingen

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 27, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change falls in intron 2 of the TYR gene. It does not directly change the encoded amino acid sequence of the TYR protein. This variant is present in population databases (rs61754381, gnomAD 1.6%), and has an allele count higher than expected for a pathogenic variant. This variant has been observed in individual(s) with oculocutaneous albinism (OCA) (PMID: 9163730, 13680365, 18463683, 19626598, 29345414). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as IVS2-7T>A. ClinVar contains an entry for this variant (Variation ID: 99527). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. -

Jun 19, 2023

Revvity Omics, Revvity

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

-

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Apr 30, 2018

Eurofins Ntd Llc (ga)

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Oct 18, 2024

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 18326704, 13680365, 22294196, 26474496, 28451379, 28266639, 32411182, 8217557, 25525159, 11041370, 25919014, 18463683, 15381243, 28629449, 19060277, 19865097, 20861488, 24721949, 28555837, 30609409, 30868578, 31077556, 28976636, 30996339, 31229681, 31980526, 36964972, 36460718, 37217489, 34426522, 31589614, 10559577, 34008892, 33223529, 33808351, Moon[case report], 35328057, 34838614, 35923705, 33834455, 35052368, 34697415, 32552135) -

-

Retina International

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

- -

Oculocutaneous albinism type 1A Pathogenic:8

Jan 03, 2022

3billion

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The variant has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least 2 similarly affected unrelated individuals(PMID: 15381243, 18463683, 22294196, 25919014, 28629449, 24721949, 18326704, PM3_S). In silico prediction tools predicted that this variant influenced pre-mRNA splicing, resulting in aberrant splicing (SPLICEAI: 0.95>=0.8, PP3_P). The variant has been reported at least twice as pathogenic/likely pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000099527). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000861, PM2_M). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -

Jul 22, 2021

Genome-Nilou Lab

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 20, 2019

Hadassah Hebrew University Medical Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Neuberg Centre For Genomic Medicine, NCGM

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The splice region variant c.1037-7T>A in TYR (NM_000372.5) has been reported to ClinVar as Pathogenic/Likely Pathogenic with a status of (2 stars) criteria provided, multiple submitters, no conflicts. The c.1037-7T>A in TYR (NM_000372.5) has an allele frequency of 0.015 in Ashkenazi Jewish subpopulation in the gnomAD database. The c.1037-7T>A variant in the TYR gene has been reported previously in both the compound heterozygous and apparently homozygous state in multiple individuals with oculocutaneous albinism type 1 (Hutton and Spritz, 2008; Ko et al., 2012; Wang et al, 2015). This variant is predicted to create a cryptic spice acceptor site and loss of the natural splice acceptor site in intron 2. An exon trapping system found that the c.1037-7T>A variant caused the insertion of 4 base pairs upstream of the common acceptor site for exon 3, resulting in a premature termination codon downstream from this variant (Goto et al., 2004). -

Oct 01, 2021

Laboratory of Medical Genetics, National & Kapodistrian University of Athens

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PM1, PM2, PP2, PP4, PP5 -

Aug 23, 2022

MGZ Medical Genetics Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 26, 2015

Genetic Services Laboratory, University of Chicago

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 06, 2020

Reproductive Health Research and Development, BGI Genomics

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: curation

NG_008748.1(NM_000372.4):c.1037-7T>A in the TYR gene has an allele frequency of 0.015 in Ashkenazi Jewish subpopulation in the gnomAD database. The c.1037-7T>A variant in the TYR gene has been reported previously in both the compound heterozygous and apparently homozygous state in multiple individuals with oculocutaneous albinism type 1 (PMID: 15381243; 18463683; 22294196; 25919014). Using an in vitro assay in A375 cells, Goto et al. (2004) demonstrated that the c.1037-7T>A/c.1037-10delTT double variant causes abnormal splicing (PMID: 15381243). Taken together, we interprete this variant as Pathogenic/Likely pathogenic. ACMG/AMP Criteria applied: PM3_Strong; PS3; PP4. -

Oculocutaneous albinism type 1B Pathogenic:4

May 10, 2018

Laboratory of Medical Genetics, National & Kapodistrian University of Athens

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PS3,PS4,PM1 -

Aug 23, 2021

Institute of Human Genetics, Heidelberg University

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

Neuberg Centre For Genomic Medicine, NCGM

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The TYR c.1037-7T>A splice-region variant has been previously reported in a total of 17 patients with oculocutaneous albinism ( Hutton et al, 2008). Using an in vitro assay in A375 cells, it was observed that the c.1037-7T>A/c.1037-10delTT double variant causes abnormal splicing ( Goto et al, 2004 ). The c.1037-7T>A variant is observed in 153/10,040 (1.5239%) alleles from individuals of Ashkenazi Jewish background in gnomAD Exomes. The nucleotide c.1037-7T>A in TYR is not conserved according to a GERP++ and PhyloP analysis of 100 vertebrates. For these reasons, this variant has been classified as Pathogenic. -

-

Pele Pequeno Principe Research Institute, Faculdades Pequeno Principe

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

- -

Oculocutaneous albinism type 1B;C4551504:Oculocutaneous albinism type 1A Pathogenic:4

Aug 07, 2023

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

- -

Feb 09, 2023

New York Genome Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The homozygous c.1037-7T>A variant identified in the TYR gene is a non-canonical splice site variant at the -7 position within intron 2/4. In silico algorithm SpliceAI predicts this variant to lead to the gain of a splice acceptor site 2bp downstream of the variant (Delta score 0.95), and the Transcript inferred Pathogenicity Score (TraP) is 0.519, which is >99% score-percentile, suggesting it is probably damaging to splicing. This variant is reported by multiple independent labs in ClinVar as Pathogenic or Likely Pathogenic (VarID:99527), and it has been reported in multiple affected individuals in the literature in both homozygous state [PMID:28629449, 28266639, others], and in compound heterozygosity with a second variant in TYR [PMID:13680365, 18326704, 19060277, others]. Given its presence in many affected individuals in the literature and in silico prediction of a damaging effect on splicing the homozygous c.1037-7T>A variant identified in the TYR gene is reported as Pathogenic. -

-

Juno Genomics, Hangzhou Juno Genomics, Inc

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PM2_Supporting+PP3+PM3_VeryStrong+PP4 -

Feb 09, 2023

New York Genome Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The homozygous c.1037-7T>A variant identified in the TYR gene is a non-canonical splice site variant at the -7 position within intron 2/4. In silico algorithm SpliceAI predicts this variant to lead to the gain of a splice acceptor site 2bp downstream of the variant (Delta score 0.95), and the Transcript inferred Pathogenicity Score (TraP) is 0.519, which is >99% score-percentile, suggesting it is probably damaging to splicing. This variant is reported by multiple independent labs in ClinVar as Pathogenic or Likely Pathogenic (VarID:99527), and it has been reported in multiple affected individuals in the literature in both homozygous state [PMID:28629449, 28266639, others], and in compound heterozygosity with a second variant in TYR [PMID:13680365, 18326704, 19060277, others]. Given its presence in many affected individuals in the literature and in silico prediction of a damaging effect on splicing the homozygous c.1037-7T>A variant identified in the TYR gene is reported as Pathogenic. -

Oculocutaneous albinism Pathogenic:3

Feb 14, 2023

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: TYR c.1037-7T>A alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Two predict the variant abolishes a canonical 3' acceptor site and one predicts the variant weakens the 3' acceptor site. Four predict the variant creates a new 3' acceptor site upstream from the canonical splice site. At least one publication reports experimental evidence that this variant indeed affects mRNA splicing by generating an abnormal splicing site, resulting in the insertion of 4 nucleotides which creates a premature termination codon downstream (e.g. Goto_2004). The variant allele was found at a frequency of 0.00095 in 249548 control chromosomes in the gnomAD database, including 1 homozygote. This frequency is not significantly higher than estimated for a pathogenic variant in TYR causing Oculocutaneous Albinism (0.00095 vs 0.0056), allowing no conclusion about variant significance. c.1037-7T>A has been reported in the literature in the homozygous and compound heterozygous state in multiple individuals affected with Oculocutaneous Albinism (e.g. Goto_2004, Lasseaux_2018). These data indicate that the variant is very likely to be associated with disease. Twenty-one submitters have provided clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as pathogenic (n=19)/likely pathogenic (n=2). Based on the evidence outlined above, the variant was classified as pathogenic. -

Feb 07, 2018

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1037-7T>A (NM_000372.4) variant in TYR has been reported in at least 9 hom ozygous and 16 compound heterozygous individuals with oculocutaneous albinism ty pe 1 (OCA1) and segregated in an affected family member (Hutton 2008a, Hutton 2 008b, Gronskov 2009, Gargiulo 2011, Shahzad 2017, Fabos 2017, and Gao 2017). It has been reported as likely pathogenic or pathogenic in ClinVar (Variation ID#99 527) by multiple laboratories. This variant has been identified in 0.04% (49/126 ,124) of European chromosomes by the Genome Aggregation Database (gnomAD http:// gnomAD.broadinstitute.org; dbSNP rs61754381). This variant has also been identif ied in 1.5% (159/10108) of Ashkenazi chromosomes including 1 homozygote by the G enome Aggregation Database (gnomAD http://gnomAD.broadinstitute.org; dbSNP rs617 54381), which is consistent with some evidence suggesting it may be a founder mu tation in this population (Blumenfeld 2008, conference abstract: http://iovs.arv ojournals.org/article.aspx?articleid=2376752). This variant is located in the 3' splice region. Computational tools suggest an impact to splicing. However, this information is not predictive enough to determine pathogenicity. In summary, al though additional studies are needed to fully establish its clinical significanc e, this variant is likely as pathogenic for OCA1 in an autosomal recessive manne r based upon multiple biallelic case observations and segregation in affected in dividuals. ACMG/AMP Criteria applied: PM3_VS, PS3_M. -

Apr 27, 2017

Illumina Laboratory Services, Illumina

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The TYR c.1037-7T>A splice-region variant has been reported in a total of 17 patients with oculocutaneous albinism (OCA), including three homozygotes, eleven compound heterozygotes, and three heterozygotes from a total of 264 affected Caucasian individuals (Hutton et al. 2008; Hutton et al. 2008; Gronskov et al. 2009; Gargiulo et al. 2011). Amongst individuals of Asian ancestry, this variant has been observed in cis with another intronic variant, c.1037-10delTT. This double variant has been reported in at least 13 affected individuals, including 11 compound heterozygotes and two heterozygotes, from a total of 194 affected Asian individuals (Goto et al. 2004; Wei et al. 2010; Ko et al. 2012; Lin et al. 2014; Wang et al. 2015). The c.1037-7T>A variant was absent from over 300 total controls, but is reported at a frequency of 0.00434 in the admixed American population of the 1000 Genomes Project. Using an in vitro assay in A375 cells, Goto et al. (2004) demonstrated that the c.1037-7T>A/c.1037-10delTT double variant causes abnormal splicing. Based on the evidence, the c.1037-7T>A variant is classified as pathogenic for oculocutaneous albinism. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -

Inborn genetic diseases Pathogenic:1

Mar 14, 2025

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1037-7T>A intronic alteration results from a T to A substitution 7 nucleotides before coding exon 3 of the TYR gene. Based on data from gnomAD, the A allele has an overall frequency of 0.086% (242/280938) total alleles studied. The highest observed frequency was 1.501% (155/10330) of Ashkenazi Jewish alleles. This variant has been identified in the homozygous state and in conjunction with other TYR variants in multiple individuals with features consistent with TYR-related oculocutaneous albinism; in at least one instance, the variants were identified in trans (Hutton, 2008; Wei, 2022; Lasseaux, 2018). This nucleotide position is not well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration may weaken the native splice acceptor site and will result in the creation or strengthening of a novel splice acceptor site. Based on the available evidence, this alteration is classified as pathogenic. -

Nonsyndromic Oculocutaneous Albinism Pathogenic:1

Mar 07, 2017

University of Washington Center for Mendelian Genomics, University of Washington

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

Albinism;C0027092:Myopia;C0028738:Nystagmus Pathogenic:1

Jan 01, 2017

Centre for Mendelian Genomics, University Medical Centre Ljubljana

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

TYR-related disorder Pathogenic:1

May 03, 2024

PreventionGenetics, part of Exact Sciences

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The TYR c.1037-7T>A variant is predicted to interfere with splicing. This variant has been reported in many individuals with oculocutaneous albinism (see for examples Hutton and Spritz 2008. PubMed ID: 18463683; Wang et al. 2015. PubMed ID: 25919014; Marti et al. 2017. PubMed ID: 28976636; Moon et al. 2022. PubMed ID: 35052368). A functional study using an exon trapping assay demonstrated that this variant causes abnormal splicing leading to premature protein termination (Goto et al. 2004. PubMed ID: 15381243, Fig. 5 reported as IVS2-10deltt-7t-a). Given all the evidence, we interpret c.1037-7T>A as pathogenic. -

Oculocutaneous albinism type 1B;C2677190:SKIN/HAIR/EYE PIGMENTATION 3, LIGHT/DARK SKIN;C4551504:Oculocutaneous albinism type 1A Pathogenic:1

May 31, 2024

Fulgent Genetics, Fulgent Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Abnormality of the skin Pathogenic:1

Jul 10, 2021

Kariminejad - Najmabadi Pathology & Genetics Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Albinism or congenital nystagmus Pathogenic:1

Nov 11, 2024

NHS Central & South Genomic Laboratory Hub

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

See cases Pathogenic:1

Dec 20, 2021

Institute of Human Genetics, University Hospital Muenster

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ACMG categories: PS1,PM1,PM3,PP3,PP5 -

SKIN/HAIR/EYE PIGMENTATION 3, LIGHT/DARK SKIN Pathogenic:1

Mar 30, 2024

Baylor Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	19
DANN	Benign	0.39

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.98
SpliceAI score (max)		0.95		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.95		Position offset: 2
DS_AL_spliceai		0.29		Position offset: 7

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs61754381; hg19: chr11-88960984;