rs2298585
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006138.5(MS4A3):c.615+44C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00936 in 1,435,424 control chromosomes in the GnomAD database, including 569 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: 𝑓 0.024 ( 124 hom., cov: 32)
Exomes 𝑓: 0.0077 ( 445 hom. )
Consequence
MS4A3
NM_006138.5 intron
NM_006138.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.139
Genes affected
MS4A3 (HGNC:7317): (membrane spanning 4-domains A3) This gene encodes a member of the membrane-spanning 4A gene family. Members of this 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. This family member likely plays a role in signal transduction and may function as a subunit associated with receptor complexes. The gene encoding this protein is localized to 11q12, among a cluster of related family members. Alternative splicing may result in multiple transcript variants; however, not all variants have been fully described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MS4A3 | NM_006138.5 | c.615+44C>T | intron_variant | ENST00000278865.8 | |||
MS4A3 | NM_001031666.2 | c.246+44C>T | intron_variant | ||||
MS4A3 | NM_001031809.2 | c.477+44C>T | intron_variant | ||||
MS4A3 | XM_011545363.4 | c.435+44C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MS4A3 | ENST00000278865.8 | c.615+44C>T | intron_variant | 1 | NM_006138.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0237 AC: 3603AN: 152126Hom.: 124 Cov.: 32
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GnomAD3 exomes AF: 0.0159 AC: 3984AN: 249952Hom.: 166 AF XY: 0.0142 AC XY: 1914AN XY: 135116
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GnomAD4 exome AF: 0.00766 AC: 9827AN: 1283180Hom.: 445 Cov.: 18 AF XY: 0.00756 AC XY: 4894AN XY: 647204
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GnomAD4 genome ? AF: 0.0237 AC: 3612AN: 152244Hom.: 124 Cov.: 32 AF XY: 0.0242 AC XY: 1800AN XY: 74456
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at