chr3-149520981-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_015472.6(WWTR1):c.1027G>A(p.Ala343Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000188 in 1,592,278 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★).
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.1027G>A | p.Ala343Thr | missense_variant | 7/7 | ENST00000360632.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WWTR1 | ENST00000360632.8 | c.1027G>A | p.Ala343Thr | missense_variant | 7/7 | 1 | NM_015472.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152152Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000613 AC: 14AN: 228260Hom.: 0 AF XY: 0.0000486 AC XY: 6AN XY: 123444
GnomAD4 exome AF: 0.0000181 AC: 26AN: 1440008Hom.: 0 Cov.: 30 AF XY: 0.0000223 AC XY: 16AN XY: 715950
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152270Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 17, 2024 | The c.1027G>A (p.A343T) alteration is located in exon 7 (coding exon 6) of the WWTR1 gene. This alteration results from a G to A substitution at nucleotide position 1027, causing the alanine (A) at amino acid position 343 to be replaced by a threonine (T). 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