11-60093449-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000139.5(MS4A2):c.428C>T(p.Thr143Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00286 in 1,614,104 control chromosomes in the GnomAD database, including 113 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_000139.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MS4A2 | ENST00000278888.8 | c.428C>T | p.Thr143Met | missense_variant | Exon 5 of 7 | 1 | NM_000139.5 | ENSP00000278888.3 | ||
MS4A2 | ENST00000617306.1 | c.293C>T | p.Thr98Met | missense_variant | Exon 4 of 6 | 1 | ENSP00000482594.1 | |||
MS4A2 | ENST00000440896.2 | n.530C>T | non_coding_transcript_exon_variant | Exon 5 of 5 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0143 AC: 2178AN: 152098Hom.: 60 Cov.: 32
GnomAD3 exomes AF: 0.00395 AC: 992AN: 251454Hom.: 27 AF XY: 0.00274 AC XY: 372AN XY: 135902
GnomAD4 exome AF: 0.00166 AC: 2428AN: 1461888Hom.: 52 Cov.: 32 AF XY: 0.00148 AC XY: 1077AN XY: 727246
GnomAD4 genome AF: 0.0143 AC: 2182AN: 152216Hom.: 61 Cov.: 32 AF XY: 0.0134 AC XY: 998AN XY: 74432
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at