chr11-60070226-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_006138.5(MS4A3):c.638C>T(p.Ser213Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000005 in 1,599,366 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006138.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MS4A3 | NM_006138.5 | c.638C>T | p.Ser213Phe | missense_variant | 7/7 | ENST00000278865.8 | |
MS4A3 | NM_001031809.2 | c.500C>T | p.Ser167Phe | missense_variant | 6/6 | ||
MS4A3 | NM_001031666.2 | c.269C>T | p.Ser90Phe | missense_variant | 5/5 | ||
MS4A3 | XM_011545363.4 | c.458C>T | p.Ser153Phe | missense_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MS4A3 | ENST00000278865.8 | c.638C>T | p.Ser213Phe | missense_variant | 7/7 | 1 | NM_006138.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000671 AC: 1AN: 149080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000125 AC: 3AN: 239522Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 129418
GnomAD4 exome AF: 0.00000483 AC: 7AN: 1450286Hom.: 0 Cov.: 29 AF XY: 0.00000277 AC XY: 2AN XY: 722142
GnomAD4 genome AF: 0.00000671 AC: 1AN: 149080Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 72690
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 30, 2022 | The c.638C>T (p.S213F) alteration is located in exon 7 (coding exon 6) of the MS4A3 gene. This alteration results from a C to T substitution at nucleotide position 638, causing the serine (S) at amino acid position 213 to be replaced by a phenylalanine (F). 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