3-149572959-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_015472.6(WWTR1):c.473C>T(p.Ala158Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,612,682 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015472.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WWTR1 | NM_015472.6 | c.473C>T | p.Ala158Val | missense_variant | 3/7 | ENST00000360632.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WWTR1 | ENST00000360632.8 | c.473C>T | p.Ala158Val | missense_variant | 3/7 | 1 | NM_015472.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151896Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249500Hom.: 1 AF XY: 0.0000371 AC XY: 5AN XY: 134764
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1460786Hom.: 1 Cov.: 32 AF XY: 0.0000248 AC XY: 18AN XY: 726642
GnomAD4 genome AF: 0.0000329 AC: 5AN: 151896Hom.: 0 Cov.: 31 AF XY: 0.0000270 AC XY: 2AN XY: 74154
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2024 | The c.473C>T (p.A158V) alteration is located in exon 3 (coding exon 2) of the WWTR1 gene. This alteration results from a C to T substitution at nucleotide position 473, causing the alanine (A) at amino acid position 158 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