rs17110761
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000350.3(ABCA4):c.6282+7G>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 0.0725 in 1,614,088 control chromosomes in the GnomAD database, including 6,526 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000350.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.127 AC: 19386AN: 152132Hom.: 2075 Cov.: 33
GnomAD3 exomes AF: 0.0766 AC: 19243AN: 251212Hom.: 1218 AF XY: 0.0727 AC XY: 9870AN XY: 135804
GnomAD4 exome AF: 0.0668 AC: 97609AN: 1461836Hom.: 4453 Cov.: 32 AF XY: 0.0667 AC XY: 48520AN XY: 727214
GnomAD4 genome AF: 0.127 AC: 19407AN: 152252Hom.: 2073 Cov.: 33 AF XY: 0.125 AC XY: 9287AN XY: 74448
ClinVar
Submissions by phenotype
not provided Benign:4Other:1
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not specified Benign:3
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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Retinitis Pigmentosa, Recessive Benign:1
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Stargardt Disease, Recessive Benign:1
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ABCA4-related disorder Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Cone-Rod Dystrophy, Recessive Benign:1
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Severe early-childhood-onset retinal dystrophy;C1858806:Cone-rod dystrophy 3;C1866422:Retinitis pigmentosa 19;C3495438:Age related macular degeneration 2 Benign:1
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Macular degeneration Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at