11-60386732-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021201.5(MS4A7):āc.298T>Gā(p.Ser100Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,613,172 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_021201.5 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 |
---|---|---|---|---|---|---|---|
MS4A7 | NM_021201.5 | c.298T>G | p.Ser100Ala | missense_variant | 4/7 | ENST00000300184.8 | |
MS4A7 | NM_206939.2 | c.298T>G | p.Ser100Ala | missense_variant | 4/7 | ||
MS4A7 | NM_206938.2 | c.163T>G | p.Ser55Ala | missense_variant | 3/6 | ||
MS4A7 | NM_206940.2 | c.163T>G | p.Ser55Ala | missense_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MS4A7 | ENST00000300184.8 | c.298T>G | p.Ser100Ala | missense_variant | 4/7 | 1 | NM_021201.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152248Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 250946Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135634
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1460924Hom.: 0 Cov.: 29 AF XY: 0.0000275 AC XY: 20AN XY: 726796
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152248Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74388
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2024 | The c.298T>G (p.S100A) alteration is located in exon 4 (coding exon 3) of the MS4A7 gene. This alteration results from a T to G substitution at nucleotide position 298, causing the serine (S) at amino acid position 100 to be replaced by an alanine (A). 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