chr6-35017512-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015245.3(ANKS1A):c.1463C>T(p.Ala488Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000101 in 1,613,436 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 Uncertain significance (★).
Frequency
Consequence
NM_015245.3 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 | UniProt |
---|---|---|---|---|---|---|---|
ANKS1A | NM_015245.3 | c.1463C>T | p.Ala488Val | missense_variant | 11/24 | ENST00000360359.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKS1A | ENST00000360359.5 | c.1463C>T | p.Ala488Val | missense_variant | 11/24 | 1 | NM_015245.3 | ||
ANKS1A | ENST00000649117.1 | c.1526C>T | p.Ala509Val | missense_variant | 12/25 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152234Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000364 AC: 9AN: 247124Hom.: 0 AF XY: 0.0000299 AC XY: 4AN XY: 133956
GnomAD4 exome AF: 0.000107 AC: 157AN: 1461202Hom.: 0 Cov.: 31 AF XY: 0.0000949 AC XY: 69AN XY: 726876
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152234Hom.: 0 Cov.: 31 AF XY: 0.0000403 AC XY: 3AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 09, 2021 | The c.1463C>T (p.A488V) alteration is located in exon 11 (coding exon 11) of the ANKS1A gene. This alteration results from a C to T substitution at nucleotide position 1463, causing the alanine (A) at amino acid position 488 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at