chr6-35017482-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BP4_Strong
The NM_015245.3(ANKS1A):c.1433G>A(p.Arg478Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000418 in 1,602,080 control chromosomes in the GnomAD database, including 2 homozygotes. 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R478W) has been classified 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 -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKS1A | NM_015245.3 | c.1433G>A | p.Arg478Gln | missense_variant | 11/24 | ENST00000360359.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKS1A | ENST00000360359.5 | c.1433G>A | p.Arg478Gln | missense_variant | 11/24 | 1 | NM_015245.3 | ||
ANKS1A | ENST00000649117.1 | c.1496G>A | p.Arg499Gln | missense_variant | 12/25 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152168Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000794 AC: 19AN: 239262Hom.: 1 AF XY: 0.000115 AC XY: 15AN XY: 129926
GnomAD4 exome AF: 0.0000393 AC: 57AN: 1449912Hom.: 2 Cov.: 31 AF XY: 0.0000472 AC XY: 34AN XY: 719926
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152168Hom.: 0 Cov.: 31 AF XY: 0.000121 AC XY: 9AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.1433G>A (p.R478Q) alteration is located in exon 11 (coding exon 11) of the ANKS1A gene. This alteration results from a G to A substitution at nucleotide position 1433, causing the arginine (R) at amino acid position 478 to be replaced by a glutamine (Q). 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