chr11-60386747-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_021201.5(MS4A7):c.313T>A(p.Ser105Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000057 in 1,613,356 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 (★).
Frequency
Consequence
NM_021201.5 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 |
---|---|---|---|---|---|---|---|
MS4A7 | NM_021201.5 | c.313T>A | p.Ser105Thr | missense_variant | 4/7 | ENST00000300184.8 | |
MS4A7 | NM_206939.2 | c.313T>A | p.Ser105Thr | missense_variant | 4/7 | ||
MS4A7 | NM_206938.2 | c.178T>A | p.Ser60Thr | missense_variant | 3/6 | ||
MS4A7 | NM_206940.2 | c.178T>A | p.Ser60Thr | missense_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MS4A7 | ENST00000300184.8 | c.313T>A | p.Ser105Thr | missense_variant | 4/7 | 1 | NM_021201.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000837 AC: 21AN: 250970Hom.: 0 AF XY: 0.0000737 AC XY: 10AN XY: 135638
GnomAD4 exome AF: 0.0000561 AC: 82AN: 1461032Hom.: 0 Cov.: 29 AF XY: 0.0000495 AC XY: 36AN XY: 726852
GnomAD4 genome AF: 0.0000656 AC: 10AN: 152324Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74492
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 19, 2024 | The c.313T>A (p.S105T) alteration is located in exon 4 (coding exon 3) of the MS4A7 gene. This alteration results from a T to A substitution at nucleotide position 313, causing the serine (S) at amino acid position 105 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