chr6-35017616-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_015245.3(ANKS1A):c.1567G>A(p.Ala523Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,613,668 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A523P) has been classified as Likely benign.
Frequency
Consequence
NM_015245.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKS1A | NM_015245.3 | c.1567G>A | p.Ala523Thr | missense_variant | 11/24 | ENST00000360359.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKS1A | ENST00000360359.5 | c.1567G>A | p.Ala523Thr | missense_variant | 11/24 | 1 | NM_015245.3 | ||
ANKS1A | ENST00000649117.1 | c.1630G>A | p.Ala544Thr | missense_variant | 12/25 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152120Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249350Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 134996
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461548Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727086
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152120Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74316
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 21, 2021 | 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