chr11-60069635-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006138.5(MS4A3):āc.575T>Cā(p.Ile192Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,288 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_006138.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MS4A3 | NM_006138.5 | c.575T>C | p.Ile192Thr | missense_variant | 6/7 | ENST00000278865.8 | |
MS4A3 | NM_001031809.2 | c.437T>C | p.Ile146Thr | missense_variant | 5/6 | ||
MS4A3 | NM_001031666.2 | c.206T>C | p.Ile69Thr | missense_variant | 4/5 | ||
MS4A3 | XM_011545363.4 | c.395T>C | p.Ile132Thr | missense_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MS4A3 | ENST00000278865.8 | c.575T>C | p.Ile192Thr | missense_variant | 6/7 | 1 | NM_006138.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251388Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135850
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461288Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726988
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.575T>C (p.I192T) alteration is located in exon 6 (coding exon 5) of the MS4A3 gene. This alteration results from a T to C substitution at nucleotide position 575, causing the isoleucine (I) at amino acid position 192 to be replaced by a threonine (T). 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