7-117320668-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003391.3(WNT2):c.209C>T(p.Ala70Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000434 in 1,613,856 control chromosomes in the GnomAD database, including 2 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_003391.3 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 |
---|---|---|---|---|---|---|---|
WNT2 | NM_003391.3 | c.209C>T | p.Ala70Val | missense_variant | 2/5 | ENST00000265441.8 | |
LOC105375467 | XR_007060645.1 | n.80-1390G>A | intron_variant, non_coding_transcript_variant | ||||
WNT2 | NR_024047.2 | n.278C>T | non_coding_transcript_exon_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WNT2 | ENST00000265441.8 | c.209C>T | p.Ala70Val | missense_variant | 2/5 | 1 | NM_003391.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152186Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000799 AC: 20AN: 250346Hom.: 0 AF XY: 0.0000886 AC XY: 12AN XY: 135380
GnomAD4 exome AF: 0.0000417 AC: 61AN: 1461552Hom.: 1 Cov.: 31 AF XY: 0.0000385 AC XY: 28AN XY: 727010
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152304Hom.: 1 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74470
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 02, 2024 | The c.209C>T (p.A70V) alteration is located in exon 2 (coding exon 2) of the WNT2 gene. This alteration results from a C to T substitution at nucleotide position 209, causing the alanine (A) at amino acid position 70 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