1-94120994-G-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_000350.3(ABCA4):c.52C>A(p.Arg18Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000096 in 1,457,948 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000096 ( 1 hom. )
Consequence
ABCA4
NM_000350.3 synonymous
NM_000350.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.243
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]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
Variant 1-94120994-G-T is Benign according to our data. Variant chr1-94120994-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 1672762.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.243 with no splicing effect.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| ABCA4 | ENST00000370225.4 | c.52C>A | p.Arg18Arg | synonymous_variant | Exon 1 of 50 | 1 | NM_000350.3 | ENSP00000359245.3 | ||
| ABCA4 | ENST00000649773.1 | c.52C>A | p.Arg18Arg | synonymous_variant | Exon 1 of 19 | ENSP00000496882.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD2 exomes AF: 0.0000358 AC: 9AN: 251400 AF XY: 0.0000221 show subpopulations
GnomAD2 exomes
AF:
AC:
9
AN:
251400
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000960 AC: 14AN: 1457948Hom.: 1 Cov.: 33 AF XY: 0.00000827 AC XY: 6AN XY: 725230 show subpopulations
GnomAD4 exome
AF:
AC:
14
AN:
1457948
Hom.:
Cov.:
33
AF XY:
AC XY:
6
AN XY:
725230
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33368
American (AMR)
AF:
AC:
1
AN:
44582
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26022
East Asian (EAS)
AF:
AC:
8
AN:
39460
South Asian (SAS)
AF:
AC:
2
AN:
86224
European-Finnish (FIN)
AF:
AC:
0
AN:
53170
Middle Eastern (MID)
AF:
AC:
0
AN:
5742
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1109264
Other (OTH)
AF:
AC:
1
AN:
60116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.487
Heterozygous variant carriers
0
1
2
4
5
6
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
31
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Mar 01, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at