chr11-60393790-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_021201.5(MS4A7):āc.652T>Cā(p.Ser218Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000106 in 1,607,806 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_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.652T>C | p.Ser218Pro | missense_variant | 7/7 | ENST00000300184.8 | |
MS4A7 | NM_206939.2 | c.652T>C | p.Ser218Pro | missense_variant | 7/7 | ||
MS4A7 | NM_206938.2 | c.517T>C | p.Ser173Pro | missense_variant | 6/6 | ||
MS4A7 | NM_206940.2 | c.517T>C | p.Ser173Pro | missense_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MS4A7 | ENST00000300184.8 | c.652T>C | p.Ser218Pro | missense_variant | 7/7 | 1 | NM_021201.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000244 AC: 6AN: 245698Hom.: 0 AF XY: 0.00000753 AC XY: 1AN XY: 132730
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1455640Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1AN XY: 724108
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 11, 2023 | The c.652T>C (p.S218P) alteration is located in exon 7 (coding exon 6) of the MS4A7 gene. This alteration results from a T to C substitution at nucleotide position 652, causing the serine (S) at amino acid position 218 to be replaced by a proline (P). 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