NM_000350.3:c.5714+5G>A

Variant names:

• chr1-94010795-C-T
• rs61751407
• NM_000350.3:c.5714+5G>A

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PP3_Moderate PP5_Very_Strong

The NM_000350.3(ABCA4):​c.5714+5G>A variant causes a splice region, intron change. The variant allele was found at a frequency of 0.000416 in 1,614,076 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.00035 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00042 (0 hom.)
• Consequence: ABCA4 NM_000350.3 splice_region, intron
• Scores: Splicing: ADA: 0.9997
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:33 O:2
• Conservation: PhyloP100: 4.06

Genes affected

ABCA4 (HGNC:34): (ATP binding cassette subfamily A member 4) The membrane-associated protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intracellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the ABC1 subfamily. Members of the ABC1 subfamily comprise the only major ABC subfamily found exclusively in multicellular eukaryotes. This protein is a retina-specific ABC transporter with N-retinylidene-PE as a substrate. It is expressed exclusively in retina photoreceptor cells, and the gene product mediates transport of an essental molecule, all-trans-retinal aldehyde (atRAL), across the photoreceptor cell membrane. Mutations in this gene are found in patients diagnosed with Stargardt disease, a form of juvenile-onset macular degeneration. Mutations in this gene are also associated with retinitis pigmentosa-19, cone-rod dystrophy type 3, early-onset severe retinal dystrophy, fundus flavimaculatus, and macular degeneration age-related 2. [provided by RefSeq, Sep 2019]

ACMG classification

Verdict is Pathogenic. Variant got 10 ACMG points.

• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. Scorers claiming Uncertain: max_spliceai. No scorers claiming Benign.
• PP5: Variant 1-94010795-C-T is Pathogenic according to our data. Variant chr1-94010795-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 99403.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-94010795-C-T is described in Lovd as [Likely_pathogenic]. Variant chr1-94010795-C-T is described in Lovd as [Pathogenic]. Variant chr1-94010795-C-T is described in Lovd as [Pathogenic]. Variant chr1-94010795-C-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCA4	NM_000350.3	c.5714+5G>A		splice_region_variant, intron_variant	Intron 40 of 49	ENST00000370225.4	NP_000341.2
ABCA4	NM_001425324.1	c.5492+5G>A		splice_region_variant, intron_variant	Intron 39 of 48		NP_001412253.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCA4	ENST00000370225.4	c.5714+5G>A		splice_region_variant, intron_variant	Intron 40 of 49	1	NM_000350.3	ENSP00000359245.3
ABCA4	ENST00000465352.1	n.130+5G>A		splice_region_variant, intron_variant	Intron 1 of 5	5

Frequencies

GnomAD3 genomes AF: 0.000348 AC: 53 AN: 152106 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000193

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.000262

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000500

Gnomad OTH AF: 0.00144

GnomAD3 exomes AF: 0.000306 AC: 77 AN: 251312 Hom.: 0 AF XY: 0.000353 AC XY: 48 AN XY: 135852

Gnomad AFR exome AF: 0.0000615

Gnomad AMR exome AF: 0.000145

Gnomad ASJ exome AF: 0.000199

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.0000462

Gnomad NFE exome AF: 0.000581

Gnomad OTH exome AF: 0.000326

GnomAD4 exome AF: 0.000423 AC: 619 AN: 1461852 Hom.: 0 Cov.: 31 AF XY: 0.000454 AC XY: 330 AN XY: 727224

Gnomad4 AFR exome AF: 0.000119

Gnomad4 AMR exome AF: 0.000179

Gnomad4 ASJ exome AF: 0.000383

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0000187

Gnomad4 NFE exome AF: 0.000517

Gnomad4 OTH exome AF: 0.000348

GnomAD4 genome AF: 0.000348 AC: 53 AN: 152224 Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19 AN XY: 74432

Gnomad4 AFR AF: 0.000193

Gnomad4 AMR AF: 0.000261

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000500

Gnomad4 OTH AF: 0.00142

Alfa AF: 0.000382 Hom.: 2

Bravo AF: 0.000348

EpiCase AF: 0.000545

EpiControl AF: 0.00124

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:33 Other:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Severe early-childhood-onset retinal dystrophy Pathogenic:9

Aug 01, 2023

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Criteria applied: PM3_VSTR,PS4,PS3_MOD,PS1_SUP,PM2_SUP,PP1 -

Oct 08, 2024

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with Stargardt disease 1 (MIM#248200) and other inherited retinal diseases (OMIM). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0115 - Variants in this gene are known to have variable expressivity (PMID: 31522899). (I) 0209 - Splice site variant proven to affect splicing of the transcript with uncertain effect on protein sequence. A mini gene assay showed that this variant led to two products; a correctly spliced one and one with exon 40 skipped (PMID: 29162642). (SP) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (highest allele count: 672 heterozygotes, 0 homozygotes). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. It has been reported in individuals with Stargardt (PMID: 10958763) and classified as pathogenic by multiple diagnostic laboratories in ClinVar. (SP) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

May 28, 2019

Mendelics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 01, 2015

NIHR Bioresource Rare Diseases, University of Cambridge

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

Apr 08, 2021

Ocular Genomics Institute, Massachusetts Eye and Ear

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

The ABCA4 c.5714+5G>A variant was identified in an individual with retinitis pigmentosa with a presumed recessive inheritance pattern. Through a review of available evidence we were able to apply the following criteria: PVS1, PM2, PM3, PP1. Based on this evidence we have classified this variant as Pathogenic. -

Jan 22, 2015

Centre for Genomic Medicine, Manchester, Central Manchester University Hospitals

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

-

Ophthalmo-Genetics Lab, Instituto de Oftalmologia Conde de Valenciana

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

Jan 30, 2021

Institute of Medical Molecular Genetics, University of Zurich

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 01, 2016

Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Pathogenic:8 Other:1

Mar 23, 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

- -

-

Retina International

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

- -

Dec 17, 2024

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Minigene splice assays in HEK293 cells demonstrate that the c.5714+5G>A variant construct results in exon 40 skipping, which was confirmed by cDNA sequencing (PMID: 29162642, 28714225); This variant is associated with the following publications: (PMID: 37498587, 34906470, 11702214, 28365912, 32307445, 35076026, 37734845, 30903310, 30093795, 31429209, 32531858, 33706644, 34758253, 31456290, 10413692, 24265693, 25066811, 22328824, 17982420, 9466990, 21911583, 11328725, 19074458, 28341476, 26872967, 28118664, 28838317, 28044389, 29555955, 30771335, 30670881, 29925512, 31589614, 32619608, 34327195, 33302505, 32783370, 32815999, 32467599, 31980526, 32581362, 35836572, 35119454, 28714225, 35260635, 36209838, 37217489, 36460718, 29162642, 35120629, 31964843, 34321860, 36669873) -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change falls in intron 40 of the ABCA4 gene. It does not directly change the encoded amino acid sequence of the ABCA4 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs61751407, gnomAD 0.05%). This variant has been observed in individuals with autosomal recessive Stargardt disease and cone-rod dystrophy (PMID: 9466990, 10413692, 19074458). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 99403). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). 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. -

Jul 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ABCA4: PM3:Very Strong, PM2, PS3:Supporting -

May 11, 2016

Eurofins Ntd Llc (ga)

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Oct 23, 2020

Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen

Significance: Pathogenic

Review Status: criteria provided, single submitter

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

- -

Stargardt disease Pathogenic:4

Apr 01, 2018

Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

May 09, 2017

Rui Chen Lab, Baylor College of Medicine

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

Jun 23, 2019

Sharon lab, Hadassah-Hebrew University Medical Center

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

May 08, 2019

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.5714+5G>A variant in ABCA4 is one of the most common variants in ABCA4 in patients with autosomal recessive Stargardt disease, accounting for up to 16% of disease-causing variants in this gene (Cremers 1998, River 2000, Smaragda 2018, Birtel 2018). It has also been identified in 71/129064 European chromosomes by gnomAD (http://gnomad.broadinstitute.org). However, this frequency is low enough to be consistent with a recessive carrier frequency. This variant has also been reported in ClinVar (Variation ID: 99403). This variant is located in the 5' splice region, and in vitro functional studies support an impact on protein function (Rivera 2000, Sangermano 2018). In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive Stargardt disease. ACMG/AMP Criteria applied: PM3_VeryStrong, PVS1_Strong, PP1. -

Retinal dystrophy Pathogenic:3

Aug 16, 2019

Blueprint Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 01, 2023

Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Oct 04, 2024

Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

PS3,PM3(strong),PM2,PP3 -

ABCA4-related disorder Pathogenic:2

Sep 07, 2018

Illumina Laboratory Services, Illumina

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Across a selection of the available literature, the ABCA4 c.5714+5G>A variant, also referred to as IVS40+5G>A, has been identified in 26 individuals with Stargardt disease, including in one homozygote, 20 compound heterozygotes, and five heterozygotes in whom a second variant was not identified, and in six compound heterozygotes with cone-rod dystrophy (Cremers et al. 1998; Rivera et al. 2000; Gerth et al. 2002; Hargitai et al. 2005; Hwang et al. 2009; Cideciyan et al. 2009). The variant was also found in four unaffected family members in a heterozygous state. The variant was absent from 320 control individuals, but is reported at a frequency of 0.00151 in the European American population of the Exome Sequencing Project. RT-PCR analysis of transformed COS-7 cells revealed that the c.5714+5G>A variant generates both a correctly spliced and an incorrectly spliced product, suggesting aberrant splicing with a possibility of some residual activity of the ABCA4 protein (Rivera et al. 2000). Based on the collective evidence, the c.5714+5G>A variant is classified as pathogenic for ABCA4-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -

Sep 18, 2024

PreventionGenetics, part of Exact Sciences

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The ABCA4 c.5714+5G>A variant is predicted to interfere with splicing. This variant (also known as IVS40+5G>A) has been reported in individuals with inherited retinal disease (see for examples Cremers et al. 1998. PubMed ID: 9466990; Klevering et al. 2004. PubMed ID: 15494742; Birtel et al. 2018. PubMed ID: 29555955). This variant is predicted to disrupt normal splicing (SpliceAI, Jaganathan et al. 2019. PubMed ID: 30661751), and functional analysis by RT-PCR revealed that this variant indeed produces both normal and abnormal splicing products (Rivera et al. 2000. PubMed ID: 10958763). This variant is reported in 0.055% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is classified as pathogenic by multiple independent submitters to the ClinVar database (https://www.ncbi.nlm.nih.gov/clinvar/variation/99403/). We classify this variant as pathogenic. -

Retinitis pigmentosa 19 Pathogenic:2

-

Genomics England Pilot Project, Genomics England

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 23, 2015

Centre for Genomic Medicine, Manchester, Central Manchester University Hospitals

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Cone-rod dystrophy 3 Pathogenic:2

Jul 01, 2008

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Jul 23, 2015

Division of Human Genetics, Children's Hospital of Philadelphia

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

Age related macular degeneration 2 Pathogenic:1

Jun 04, 2019

Centre for Mendelian Genomics, University Medical Centre Ljubljana

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PS3,PM2,PM3,PP3. -

Optic atrophy Pathogenic:1

Jan 01, 2023

Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Severe early-childhood-onset retinal dystrophy;C1858806:Cone-rod dystrophy 3;C1866422:Retinitis pigmentosa 19;C3495438:Age related macular degeneration 2 Pathogenic:1

Jun 06, 2024

Fulgent Genetics, Fulgent Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Stargardt disease;C4085590:Cone-rod dystrophy Other:1

-

GenomeConnect, ClinGen

Significance: not provided

Review Status: no classification provided

Collection Method: phenotyping only

Variant interpretted as pathogenic and reported on 07/26/2017 by GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	16
DANN	Benign	0.91

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.99
SpliceAI score (max)		0.31		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.31		Position offset: 5

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

Publications

LitVar

Other links and lift over

dbSNP: rs61751407; hg19: chr1-94476351;