chr3-149572888-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_015472.6(WWTR1):āc.544A>Gā(p.Met182Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000575 in 1,613,950 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (ā ).
Frequency
Consequence
NM_015472.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WWTR1 | NM_015472.6 | c.544A>G | p.Met182Val | missense_variant | 3/7 | ENST00000360632.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WWTR1 | ENST00000360632.8 | c.544A>G | p.Met182Val | missense_variant | 3/7 | 1 | NM_015472.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000349 AC: 53AN: 151982Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000282 AC: 71AN: 251400Hom.: 0 AF XY: 0.000272 AC XY: 37AN XY: 135854
GnomAD4 exome AF: 0.000596 AC: 871AN: 1461850Hom.: 0 Cov.: 32 AF XY: 0.000554 AC XY: 403AN XY: 727220
GnomAD4 genome AF: 0.000375 AC: 57AN: 152100Hom.: 0 Cov.: 31 AF XY: 0.000363 AC XY: 27AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 15, 2021 | The c.544A>G (p.M182V) alteration is located in exon 3 (coding exon 2) of the WWTR1 gene. This alteration results from a A to G substitution at nucleotide position 544, causing the methionine (M) at amino acid position 182 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