rs983034
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_024911.7(WLS):c.1393G>A(p.Val465Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 1,613,486 control chromosomes in the GnomAD database, including 114,104 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_024911.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WLS | NM_024911.7 | c.1393G>A | p.Val465Ile | missense_variant | 11/12 | ENST00000262348.9 | |
GNG12-AS1 | NR_040077.1 | n.1075-394C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WLS | ENST00000262348.9 | c.1393G>A | p.Val465Ile | missense_variant | 11/12 | 1 | NM_024911.7 | P1 | |
GNG12-AS1 | ENST00000420587.5 | n.1060-394C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.307 AC: 46628AN: 151894Hom.: 8130 Cov.: 32
GnomAD3 exomes AF: 0.349 AC: 87538AN: 251104Hom.: 16384 AF XY: 0.354 AC XY: 48003AN XY: 135702
GnomAD4 exome AF: 0.375 AC: 548025AN: 1461474Hom.: 105967 Cov.: 46 AF XY: 0.376 AC XY: 273379AN XY: 727068
GnomAD4 genome ? AF: 0.307 AC: 46653AN: 152012Hom.: 8137 Cov.: 32 AF XY: 0.305 AC XY: 22648AN XY: 74294
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at