7-117531117-A-G

Variant names:

• chr7-117531117-A-G
• rs377729736
• NM_000492.4:c.489+3A>G

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PP3 PP5

The NM_000492.4(CFTR):​c.489+3A>G variant causes a splice region, intron change. The variant allele was found at a frequency of 0.000178 in 1,605,062 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.00015 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00018 (0 hom.)
• Consequence: CFTR NM_000492.4 splice_region, intron
• Scores: Splicing: ADA: 0.9994
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:16 U:8
• Conservation: PhyloP100: 4.74
• Publications: 7 publications found

Genes affected

CFTR (HGNC:1884): (CF transmembrane conductance regulator) This gene encodes a member of the ATP-binding cassette (ABC) transporter superfamily. The encoded protein functions as a chloride channel, making it unique among members of this protein family, and controls ion and water secretion and absorption in epithelial tissues. Channel activation is mediated by cycles of regulatory domain phosphorylation, ATP-binding by the nucleotide-binding domains, and ATP hydrolysis. Mutations in this gene cause cystic fibrosis, the most common lethal genetic disorder in populations of Northern European descent. The most frequently occurring mutation in cystic fibrosis, DeltaF508, results in impaired folding and trafficking of the encoded protein. Multiple pseudogenes have been identified in the human genome. [provided by RefSeq, Aug 2017]

CFTR Gene-Disease associations (from GenCC):

• cystic fibrosis

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae), Myriad Women’s Health, Orphanet
• congenital bilateral absence of vas deferens

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
• hereditary chronic pancreatitis

  Inheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PP3: Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 7-117531117-A-G is Pathogenic according to our data. Variant chr7-117531117-A-G is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 53971.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000492.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFTR	NM_000492.4	MANE Select	c.489+3A>G		splice_region intron	N/A	NP_000483.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFTR	ENST00000003084.11	TSL:1 MANE Select	c.489+3A>G		splice_region intron	N/A	ENSP00000003084.6
	CFTR	ENST00000699602.1		c.489+3A>G		splice_region intron	N/A	ENSP00000514471.1
	CFTR	ENST00000426809.5	TSL:5	c.489+3A>G		splice_region intron	N/A	ENSP00000389119.1

Frequencies

GnomAD3 genomes AF: 0.000151 AC: 23 AN: 152196 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000724

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000655

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000250

Gnomad OTH AF: 0.000478

GnomAD2 exomes AF: 0.000249 AC: 61 AN: 245226 AF XY: 0.000302

Gnomad AFR exome AF: 0.0000628

Gnomad AMR exome AF: 0.000294

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000469

Gnomad NFE exome AF: 0.000427

Gnomad OTH exome AF: 0.000334

GnomAD4 exome AF: 0.000180 AC: 262 AN: 1452866 Hom.: 0 Cov.: 29 AF XY: 0.000181 AC XY: 131 AN XY: 722966

African (AFR) AF: 0.0000300 AC: 1 AN: 33318

American (AMR) AF: 0.000293 AC: 13 AN: 44404

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25980

East Asian (EAS) AF: 0.00 AC: 0 AN: 39600

South Asian (SAS) AF: 0.0000234 AC: 2 AN: 85596

European-Finnish (FIN) AF: 0.0000377 AC: 2 AN: 53074

Middle Eastern (MID) AF: 0.00104 AC: 6 AN: 5750

European-Non Finnish (NFE) AF: 0.000205 AC: 227 AN: 1105090

Other (OTH) AF: 0.000183 AC: 11 AN: 60054

GnomAD4 genome AF: 0.000151 AC: 23 AN: 152196 Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11 AN XY: 74348

African (AFR) AF: 0.0000724 AC: 3 AN: 41454

American (AMR) AF: 0.0000655 AC: 1 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5198

South Asian (SAS) AF: 0.00 AC: 0 AN: 4826

European-Finnish (FIN) AF: 0.0000942 AC: 1 AN: 10620

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.000250 AC: 17 AN: 68028

Other (OTH) AF: 0.000478 AC: 1 AN: 2094

Alfa AF: 0.000340 Hom.: 0

Bravo AF: 0.000181

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:16 Uncertain:8

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Cystic fibrosis Pathogenic:9 Uncertain:2

Jul 03, 2025

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

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: CFTR c.489+3A>G, legacy name c.621+3A>G, alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 4/4 in silico tools via Alamut predict that the variant abolishes or weakens the canonical 5' splicing donor site. This is further supported by experimental evidence reporting an impact on mRNA splicing as corroborated by two independent studies that showed a reproducible distribution of transcripts resulting from activation of an alternate splice site (approx 28.3%) and transcripts resulting from complete skipping of exon 4 (approx 6.8%) in addition to levels of wild-type transcripts (approx remaining 65%) (Tzetis_2001, Forzan_2010). Furthermore, the pattern of abnormal splicing demonstrated by this variant is very similar to that of c.489+1G>T (legacy name c.621+1G>T) considered to be a well-recognized pathogenic CFTR variant (Tzetis_2001). The variant allele was found at a frequency of 0.00025 in 247812 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in CFTR causing Non-Classic Cystic Fibrosis (0.00025 vs 0.013), allowing no conclusion about variant significance. c.489+3A>G has been reported in the literature in individuals affected with Cystic Fibrosis or with a provisional CF diagnosis with intermediate sweat chloride levels (e.g. Tzetis_2001, Kanavakis_2003, Soltysova_2018, Claustres_2017, Angyal_2024) and in individuals with other CFTR-related diseases such as CBAVD (e.g. Amato_2012), azoospermia (e.g. Gallati_2009), sarcoidosis (Bombieri_2000), and chronic pancreatitis (Sofia_2016). These data, when ascertained conservatively, limited to patients with a confirmed diagnosis of CF, support the notion that the variant is likely to be associated with disease. At least one report of an asymptomatic 8 year old girl harboring this variant in trans with another pathogenic CFTR variant (p.Q552*) has been ascertained (Forzan_2010). This patient had inconsistent sweat chloride levels ranging from 49-75 mEq/L in three independent measurements and the possibility of subclinical disease cannot be entirely ruled out. In addition, the variant was also reported to have been observed in cis with c.4332delTG (legacy name) in a CF patient harboring c.2183AA/G (legacy name) on the other allele (Loumi_2008). However, to our knowledge, there are no additional reports of this co-occurrence to substantiate this finding. The following publications have been ascertained in the context of this evaluation (PMID: 26990548, 22020151, 22439019, 10980579, 28603918, 25304080, 25308578, 19893581, 20021716, 17850636, 20657600, 20932301, 12752573, 17572159, 27264265, 28544683, 11810271). The CFTR2 database states this variant to have varying consequences. ClinVar contains an entry for this variant (Variation ID: 53971). Based on the evidence outlined above, the variant was classified as likely pathogenic.

Jan 14, 2025

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.489+3A>G intronic variant results from an A to G substitution 3 nucleotides after coding exon 4 in the CFTR gene. This variant (reported as 621+3A>G) was described in four Greek individuals with severe cystic fibrosis (CF), each with a second pathogenic mutation; however, the phase of these alterations is uncertain (Tzetis M et al. Hum Genet, 2001 Dec;109:592-601). In addition, this variant has been reported with a second pathogenic variant in other individuals with intermediate sweat chloride levels (Forzan M et al. J Hum Genet, 2010 Jan;55:23-6; Sermet-Gaudelus I et al. Thorax, 2010 Jun;65:539-44; Esposito MV et al. J Clin Med, 2020 Nov;9:). However, it has also been detected in trans with a pathogenic variant in multiple individuals with normal sweat chloride levels (Ambry internal data). Functional studies using RNA from patients and minigene assay showed that this variant results in partial and full exon skipping (Tzetis M et al. Hum Genet, 2001 Dec;109:592-601; Forzan M et al. J Hum Genet, 2010 Jan;55:23-6). In another RNA study, this variant has approximately 90% of wild type quantity and function (The Clinical and Functional TRanslation of CFTR (CFTR2) database available at http://cftr2.org. Accessed 12/15/2023). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Based on available evidence to date, this variant is unlikely to be causative of classic cystic fibrosis; however, its contribution to the development of a CFTR-related disorder is uncertain. This alteration is thus classified as a variant of unknown significance.

Baylor Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Jan 13, 2022

MGZ Medical Genetics Center

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Jul 22, 2021

Genome-Nilou Lab

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

May 22, 2024

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Criteria applied: PS3_VSTR,PM3,PP4

Nov 05, 2018

Mendelics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Jan 29, 2020

Johns Hopkins Genomics, Johns Hopkins University

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

CFTR variant associated with variable clinical consequences. See www.CFTR2.org for phenotype information.

Jun 27, 2025

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: curation

The heterozygous c.489+3A>G variant in CFTR was identified by our study, in the compound heterozygous state along with a variant of uncertain significance, in 1 individual with pancreatic insufficiency. The phase of these variants are unknown at this time. The c.489+3A>G variant in CFTR has been reported in at least 4 individuals with cystic fibrosis (PMID: 11810271), and has been identified in 0.1% (6/6066) of Middle Eastern chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs377729736). Although this variant has been seen in the general population in a heterozygous state, its frequency is not high enough to rule out a pathogenic role. This variant has been reported in ClinVar (Variation ID: 53971) and has been interpreted as pathogenic by 3 submitters, likely pathogenic by 9 submitters, and a variant of uncertain significance by 6 submitters. Of the 5 affected individuals, 4 were compound heterozygotes that carried a reported pathogenic variant with unknown phase, which increases the likelihood that the c.489+3A>G variant is pathogenic (Variation ID: 7105, 7129, 7168; PMID: 11810271). Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. This variant is located in the 5' splice region. Computational tools predict a splicing impact, though this information is not predictive enough to determine/rule out pathogenicity. This variant is adjacent to an in-frame exon and is more likely to escape nonsense mediated decay (NMD) and result in a truncated protein. Minigene analysis shows evidence of exon skipping of exon 4. Exon 4 is in-frame with 72 amino acids. Loss of function of the CFTR gene is an established disease mechanism in autosomal recessive cystic fibrosis. In summary, although additional studies are required to fully establish its clinical significance, this variant is likely pathogenic for autosomal recessive cystic fibrosis. ACMG/AMP Criteria applied: PM3_strong, PVS1_moderate(Richards 2015).

Jan 21, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change falls in intron 4 of the CFTR gene. It does not directly change the encoded amino acid sequence of the CFTR protein. RNA analysis indicates that this variant induces altered splicing and likely results in a shortened protein product. This variant is present in population databases (rs377729736, gnomAD 0.04%). This variant has been observed in individual(s) with cystic fibrosis, sarcoidosis, azoospermia, or congenital absence of the vas deference (PMID: 10980579, 11810271, 19893581, 20021716, 22020151). This variant is also known as 621+3A>G. ClinVar contains an entry for this variant (Variation ID: 53971). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of 4, but is expected to preserve the integrity of the reading-frame (PMID: 11810271). For these reasons, this variant has been classified as Pathogenic.

Apr 25, 2025

Institute of Immunology and Genetics Kaiserslautern

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ACMG Criteria: PVS1_S, PM2_P, PM3, PP5; Variant was found in heterozygous state. The patient was an asymptomatic carrier.

not provided Pathogenic:1 Uncertain:5

Nov 11, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The CFTR c.489+3A>G variant (rs377729736, ClinVar Variation ID: 53971), also known as 621+3A>G, is reported in the literature in individuals affected with cystic fibrosis, congenital bilateral absence of vas deferens (CBAVD), and sarcoidosis, including individuals with a severe pathogenic variant on the opposite chromosome (Amato 2012, Angyal 2024, Gallati 2009, Giuliani 2010, Sermet-Gaudelus 2010, Soltysova 2018, Tzetis 2001). However, this variant has also been reported in an asymptomatic individual who carries a pathogenic nonsense variant in trans (Forzan 2010), and in cis with a truncating variant in an individual with cystic fibrosis (Loumi 2008). This variant is found in the general population with an overall allele frequency of 0.023% (63/276,630 alleles) in the Genome Aggregation Database (v2.1.1). Computational analyses (Alamut v.2.11) predict that this variant may impact splicing by weakening the nearby canonical donor splice site. Functional studies show aberrant mRNA splicing making up about 35% of transcripts, but it is unknown if this level altered transcripts is sufficient to cause disease (Forzan 2010, Tzetis 2001). Due to conflicting information, the clinical significance of the c.489+3A>G variant is uncertain at this time. References: Amato F et al. Extensive molecular analysis of patients bearing CFTR-related disorders. J Mol Diagn. 2012 Jan;14(1):81-9. PMID: 22020151. Angyal D et al. CFTR function is impaired in a subset of patients with pancreatitis carrying rare CFTR variants. Pancreatology. 2024 May;24(3):394-403. PMID: 38493004. Forzan M et al. Is CFTR 621+3 A>G a cystic fibrosis causing mutation? J Hum Genet. 2010 Jan;55(1):23-6. PMID: 19893581. Gallati S et al. Cystic fibrosis transmembrane conductance regulator mutations in azoospermic and oligospermic men and their partners. Reprod Biomed Online. 2009 Nov;19(5):685-94. PMID: 20021716. Giuliani R et al. Identification of the second CFTR mutation in patients with congenital bilateral absence of vas deferens undergoing ART protocols. Asian J Androl. 2010 Nov;12(6):819-26. PMID: 20657600. Loumi O et al. CFTR mutations in the Algerian population. J Cyst Fibros. 2008 Jan;7(1):54-9. Epub 2007 Jun 14. PMID: 17572159. Sermet-Gaudelus I et al. Measurement of nasal potential difference in young children with an equivocal sweat test following newborn screening for cystic fibrosis. Thorax. 2010 Jun;65(6):539-44. PMID: 20522854. Soltysova A et al. Comprehensive genetic study of cystic fibrosis in Slovak patients in 25 years of genetic diagnostics. Clin Respir J. 2018 Mar;12(3):1197-1206. PMID: 28544683. Tzetis M et al. Qualitative and quantitative analysis of mRNA associated with four putative splicing mutations (621+3A-->G, 2751+2T-->A, 296+1G-->C, 1717-9T-->C-D565G) and one nonsense mutation (E822X) in the CFTR gene. Hum Genet. 2001 Dec;109(6):592-601. PMID: 11810271.

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

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

Nov 22, 2017

Eurofins Ntd Llc (ga)

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Jul 05, 2023

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The CFTR c.489+3A>G variant has been reported in the published literature in individuals with cystic fibrosis (CF) who carried a CFTR pathogenic variant on the opposite chromosome (PMID: 11810271 (2001)). It has also been observed in individuals with sarcoidosis (PMID: 10980579 (2000)), azoospermia (PMID: 20021716 (2009)), bronchiectasis (PMID: 33260873 (2020)), and congenital bilateral absence of the vas deferens (CBAVD) (PMID: 22020151 (2012)). However, it has also been observed in an asymptomatic individual who carried a CFTR pathogenic variant on the opposite chromosome (PMID: 1989381 (2010)). RNA studies have shown that it causes the synthesis of aberrantly spliced CFTR mRNA transcripts, but it does not prevent the synthesis of normally spliced CFTR mRNA (PMID: 11810271 (2001), 19893581 (2010)). The frequency of this variant in the general population, 0.0021 (23/11152 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Analysis of this variant using software algorithms for the prediction of the effect of nucleotide changes on splicing yielded predictions that this variant may affect proper CFTR mRNA splicing. Based on the available information, this variant is classified as likely pathogenic.

Jul 28, 2017

GeneDx

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.489+3A>G variant in the CFTR gene, also referred to as c.621+3A>G, has been reported in the heterozygous state patients with sarcoidosis, CAVD, and azoospermia without CAVD (Bombieri et al., 2000; Amato et al., 2012; Gallati et al., 2009). This variant reduces the quality of the splice donor site in intron 4, and may cause abnormal gene splicing. The c.489+3A>G variant is observed in 30/50716 (0.06%) alleles in the ExAC dataset (Lek et al., 2016). We interpret c.489+3A>G as a variant of uncertain significance.

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

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

CFTR-related disorder Pathogenic:2

Mar 05, 2024

PreventionGenetics, part of Exact Sciences

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The CFTR c.489+3A>G variant is predicted to interfere with splicing. This variant has been reported in patients with cystic fibrosis, congenital bilateral absence of vas deferens (CBAVD), azoospermia, or sarcoidosis, including in patients with a pathogenic variant on the opposite chromosome (Amato et al. 2011. PubMed ID: 22020151; Bombieri et al. 2000. PubMed ID: 10980579; Gallati et al. 2009. PubMed ID: 20021716; Giuliani et al. 2010. PubMed ID: 20657600; Kanavakis et al. 2003. PubMed ID: 12752573; Sermet-Gaudelus et al. 2010. PubMed ID: 20522854; Soltysova et al. 2017. PubMed ID: 28544683; Tzetis et al. 2001. PubMed ID: 11810271). This variant was also reported in trans with a second pathogenic variant in an asymptomatic female child; however, her sweat chloride testing suggested possible subclinical disease (49-75 mEq/L) (Forzan et al. 2009. PubMed ID: 19893581). Additionally, functional studies demonstrate that this variant leads to aberrant splicing with a defect consistent with other known splicing variants at this location (c.489+1G>T aka 621+1G>T; Tzetis et al. 2001. PubMed ID: 11810271; Forzan et al. 2009. PubMed ID: 19893581). This variant is reported in 0.039% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Taken together, this variant is interpreted as likely pathogenic.

Mar 09, 2018

CFTR-France

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: curation

Hereditary pancreatitis Pathogenic:1 Uncertain:1

Oct 20, 2022

Eurofins-Biomnis

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Apr 21, 2021

Sema4, Sema4

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: curation

Cystic fibrosis;C0238339:Hereditary pancreatitis;C0403814:Congenital bilateral aplasia of vas deferens from CFTR mutation;C2749757:Bronchiectasis with or without elevated sweat chloride 1 Pathogenic:1

May 15, 2024

Fulgent Genetics, Fulgent Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Bronchiectasis with or without elevated sweat chloride 1 Pathogenic:1

Mar 28, 2024

Baylor Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Respiratory ciliopathies including non-CF bronchiectasis Pathogenic:1

Sep 25, 2025

NHS Central & South Genomic Laboratory Hub

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	17
DANN	Benign	0.97
PhyloP100		4.7
Mutation Taster		=1/99	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.95
Splicevardb		3.0
SpliceAI score (max)		0.72		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.72		Position offset: -3

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

Other links and lift over

dbSNP: rs377729736; hg19: chr7-117171171;