rs140532711
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000139.5(MS4A2):c.58G>A(p.Val20Met) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,984 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000139.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MS4A2 | ENST00000278888.8 | c.58G>A | p.Val20Met | missense_variant, splice_region_variant | Exon 2 of 7 | 1 | NM_000139.5 | ENSP00000278888.3 | ||
MS4A2 | ENST00000617306.1 | c.58G>A | p.Val20Met | missense_variant, splice_region_variant | Exon 2 of 6 | 1 | ENSP00000482594.1 | |||
MS4A2 | ENST00000440896.2 | n.160G>A | splice_region_variant, non_coding_transcript_exon_variant | Exon 2 of 5 | 1 | |||||
MS4A2 | ENST00000524868.1 | c.58G>A | p.Val20Met | missense_variant, splice_region_variant | Exon 3 of 3 | 4 | ENSP00000433311.1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251384Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135872
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461814Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727216
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.58G>A (p.V20M) alteration is located in exon 2 (coding exon 2) of the MS4A2 gene. This alteration results from a G to A substitution at nucleotide position 58, causing the valine (V) at amino acid position 20 to be replaced by a methionine (M). 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