19-48713939-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001130915.2(MAMSTR):c.830C>T(p.Ala277Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00025 in 1,613,370 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001130915.2 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAMSTR | NM_001130915.2 | c.830C>T | p.Ala277Val | missense_variant | 8/10 | ENST00000318083.11 | NP_001124387.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAMSTR | ENST00000318083.11 | c.830C>T | p.Ala277Val | missense_variant | 8/10 | 2 | NM_001130915.2 | ENSP00000324175.5 | ||
MAMSTR | ENST00000594582.1 | c.326C>T | p.Ala109Val | missense_variant | 5/7 | 1 | ENSP00000471590.1 | |||
MAMSTR | ENST00000356751.8 | c.521C>T | p.Ala174Val | missense_variant | 6/8 | 2 | ENSP00000349192.3 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000926 AC: 23AN: 248306Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 134544
GnomAD4 exome AF: 0.000270 AC: 395AN: 1461148Hom.: 0 Cov.: 42 AF XY: 0.000261 AC XY: 190AN XY: 726870
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152222Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 10, 2024 | The c.830C>T (p.A277V) alteration is located in exon 8 (coding exon 7) of the MAMSTR gene. This alteration results from a C to T substitution at nucleotide position 830, causing the alanine (A) at amino acid position 277 to be replaced by a valine (V). 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