rs12453
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_022349.4(MS4A6A):āc.327A>Gā(p.Leu109=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 1,609,884 control chromosomes in the GnomAD database, including 123,466 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.33 ( 8828 hom., cov: 31)
Exomes š: 0.39 ( 114638 hom. )
Consequence
MS4A6A
NM_022349.4 synonymous
NM_022349.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.549
Genes affected
MS4A6A (HGNC:13375): (membrane spanning 4-domains A6A) This gene encodes a member of the membrane-spanning 4A gene family. Members of this nascent protein family are characterized by common structural features and similar intron/exon splice boundaries and display unique expression patterns among hematopoietic cells and nonlymphoid tissues. The gene encoding this protein is localized to 11q12.1, among a cluster of family members. Alternative splicing of this gene results in several transcript variants that encode different protein isoforms. [provided by RefSeq, Oct 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP7
?
Synonymous conserved (PhyloP=-0.549 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MS4A6A | NM_022349.4 | c.327A>G | p.Leu109= | synonymous_variant | 4/6 | ENST00000528851.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MS4A6A | ENST00000528851.6 | c.327A>G | p.Leu109= | synonymous_variant | 4/6 | 1 | NM_022349.4 |
Frequencies
GnomAD3 genomes ? AF: 0.327 AC: 49685AN: 151922Hom.: 8824 Cov.: 31
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GnomAD3 exomes AF: 0.354 AC: 88762AN: 250862Hom.: 17076 AF XY: 0.371 AC XY: 50272AN XY: 135630
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GnomAD4 exome AF: 0.390 AC: 568807AN: 1457844Hom.: 114638 Cov.: 32 AF XY: 0.395 AC XY: 286511AN XY: 725380
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GnomAD4 genome ? AF: 0.327 AC: 49710AN: 152040Hom.: 8828 Cov.: 31 AF XY: 0.325 AC XY: 24190AN XY: 74336
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at