rs7232
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022349.4(MS4A6A):c.553A>T(p.Thr185Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 1,610,750 control chromosomes in the GnomAD database, including 104,970 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/16 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_022349.4 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 |
---|---|---|---|---|---|---|---|
MS4A6A | NM_022349.4 | c.553A>T | p.Thr185Ser | missense_variant | 6/6 | ENST00000528851.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MS4A6A | ENST00000528851.6 | c.553A>T | p.Thr185Ser | missense_variant | 6/6 | 1 | NM_022349.4 |
Frequencies
GnomAD3 genomes ? AF: 0.272 AC: 41186AN: 151360Hom.: 6920 Cov.: 32
GnomAD3 exomes AF: 0.308 AC: 77415AN: 251080Hom.: 13945 AF XY: 0.327 AC XY: 44393AN XY: 135678
GnomAD4 exome AF: 0.357 AC: 520684AN: 1459274Hom.: 98051 Cov.: 34 AF XY: 0.361 AC XY: 262326AN XY: 726034
GnomAD4 genome ? AF: 0.272 AC: 41188AN: 151476Hom.: 6919 Cov.: 32 AF XY: 0.270 AC XY: 19993AN XY: 74000
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at