chr17-69083312-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_080284.3(ABCA6):c.4375G>A(p.Val1459Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000426 in 1,595,750 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_080284.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ABCA6 | NM_080284.3 | c.4375G>A | p.Val1459Ile | missense_variant | 35/39 | ENST00000284425.7 | NP_525023.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ABCA6 | ENST00000284425.7 | c.4375G>A | p.Val1459Ile | missense_variant | 35/39 | 1 | NM_080284.3 | ENSP00000284425 | P1 | |
ABCA6 | ENST00000446604.6 | n.1641G>A | non_coding_transcript_exon_variant | 14/18 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152074Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000305 AC: 7AN: 229430Hom.: 0 AF XY: 0.0000241 AC XY: 3AN XY: 124526
GnomAD4 exome AF: 0.0000423 AC: 61AN: 1443676Hom.: 0 Cov.: 31 AF XY: 0.0000418 AC XY: 30AN XY: 718168
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152074Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74276
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 06, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at