chr6-35017481-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_015245.3(ANKS1A):c.1432C>T(p.Arg478Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000135 in 1,601,798 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R478Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_015245.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKS1A | NM_015245.3 | c.1432C>T | p.Arg478Trp | missense_variant | 11/24 | ENST00000360359.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKS1A | ENST00000360359.5 | c.1432C>T | p.Arg478Trp | missense_variant | 11/24 | 1 | NM_015245.3 | ||
ANKS1A | ENST00000649117.1 | c.1495C>T | p.Arg499Trp | missense_variant | 12/25 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000263 AC: 40AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000105 AC: 25AN: 238682Hom.: 0 AF XY: 0.0000925 AC XY: 12AN XY: 129674
GnomAD4 exome AF: 0.000122 AC: 177AN: 1449614Hom.: 0 Cov.: 31 AF XY: 0.000124 AC XY: 89AN XY: 719770
GnomAD4 genome ? AF: 0.000263 AC: 40AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.000229 AC XY: 17AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2022 | The c.1432C>T (p.R478W) 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 1432, causing the arginine (R) at amino acid position 478 to be replaced by a tryptophan (W). 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