chr3-149527912-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_015472.6(WWTR1):āc.829G>Cā(p.Ala277Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000805 in 1,613,942 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 Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WWTR1 | NM_015472.6 | c.829G>C | p.Ala277Pro | missense_variant | 5/7 | ENST00000360632.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WWTR1 | ENST00000360632.8 | c.829G>C | p.Ala277Pro | missense_variant | 5/7 | 1 | NM_015472.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251346Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135832
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461830Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 727210
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 20, 2023 | The c.829G>C (p.A277P) alteration is located in exon 5 (coding exon 4) of the WWTR1 gene. This alteration results from a G to C substitution at nucleotide position 829, causing the alanine (A) at amino acid position 277 to be replaced by a proline (P). 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