1-93993227-G-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_000350.3(ABCA4):c.*10C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00123 in 1,613,904 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_000350.3 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00624 AC: 949AN: 152164Hom.: 12 Cov.: 32
GnomAD3 exomes AF: 0.00177 AC: 445AN: 250948Hom.: 9 AF XY: 0.00134 AC XY: 182AN XY: 135598
GnomAD4 exome AF: 0.000709 AC: 1036AN: 1461622Hom.: 9 Cov.: 30 AF XY: 0.000620 AC XY: 451AN XY: 727122
GnomAD4 genome AF: 0.00625 AC: 952AN: 152282Hom.: 12 Cov.: 32 AF XY: 0.00622 AC XY: 463AN XY: 74460
ClinVar
Submissions by phenotype
not specified Benign:2
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ABCA4-related disorder Uncertain:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
not provided Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at