11-60089727-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000139.5(MS4A2):āc.92A>Cā(p.Gln31Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,614,216 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (ā ).
Frequency
Consequence
NM_000139.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MS4A2 | ENST00000278888.8 | c.92A>C | p.Gln31Pro | missense_variant | Exon 2 of 7 | 1 | NM_000139.5 | ENSP00000278888.3 | ||
MS4A2 | ENST00000617306.1 | c.92A>C | p.Gln31Pro | missense_variant | Exon 2 of 6 | 1 | ENSP00000482594.1 | |||
MS4A2 | ENST00000440896.2 | n.194A>C | non_coding_transcript_exon_variant | Exon 2 of 5 | 1 | |||||
MS4A2 | ENST00000524868.1 | c.92A>C | p.Gln31Pro | missense_variant | Exon 3 of 3 | 4 | ENSP00000433311.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152236Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000835 AC: 21AN: 251400Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135876
GnomAD4 exome AF: 0.0000287 AC: 42AN: 1461862Hom.: 0 Cov.: 31 AF XY: 0.0000330 AC XY: 24AN XY: 727234
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152354Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74516
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.92A>C (p.Q31P) alteration is located in exon 2 (coding exon 2) of the MS4A2 gene. This alteration results from a A to C substitution at nucleotide position 92, causing the glutamine (Q) at amino acid position 31 to be replaced by a proline (P). 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