chr2-100473528-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001011717.1(NMS):c.172C>T(p.Arg58Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000688 in 1,454,010 control chromosomes in the GnomAD database, including 1 homozygotes. 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 (★).
Frequency
Consequence
NM_001011717.1 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 |
---|---|---|---|---|---|---|---|
NMS | NM_001011717.1 | c.172C>T | p.Arg58Cys | missense_variant | 3/10 | ENST00000376865.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NMS | ENST00000376865.1 | c.172C>T | p.Arg58Cys | missense_variant | 3/10 | 1 | NM_001011717.1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000733 AC: 11AN: 150062Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000381 AC: 8AN: 210168Hom.: 0 AF XY: 0.0000520 AC XY: 6AN XY: 115482
GnomAD4 exome AF: 0.0000683 AC: 89AN: 1303948Hom.: 0 Cov.: 22 AF XY: 0.0000712 AC XY: 46AN XY: 645950
GnomAD4 genome ? AF: 0.0000733 AC: 11AN: 150062Hom.: 1 Cov.: 32 AF XY: 0.0000273 AC XY: 2AN XY: 73232
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2022 | The c.172C>T (p.R58C) alteration is located in exon 3 (coding exon 3) of the NMS gene. This alteration results from a C to T substitution at nucleotide position 172, causing the arginine (R) at amino acid position 58 to be replaced by a cysteine (C). 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