chr19-48714853-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.481C>T(p.Pro161Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,612,942 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 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 | UniProt |
---|---|---|---|---|---|---|---|
MAMSTR | NM_001130915.2 | c.481C>T | p.Pro161Ser | missense_variant | 6/10 | ENST00000318083.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAMSTR | ENST00000318083.11 | c.481C>T | p.Pro161Ser | missense_variant | 6/10 | 2 | NM_001130915.2 | P2 | |
MAMSTR | ENST00000594582.1 | c.172C>T | p.Pro58Ser | missense_variant | 4/7 | 1 | |||
MAMSTR | ENST00000356751.8 | c.172C>T | p.Pro58Ser | missense_variant | 4/8 | 2 | A2 | ||
MAMSTR | ENST00000599703.1 | c.631C>T | p.Pro211Ser | missense_variant | 6/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152040Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250966Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135660
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1460784Hom.: 0 Cov.: 33 AF XY: 0.0000303 AC XY: 22AN XY: 726778
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152158Hom.: 0 Cov.: 30 AF XY: 0.0000134 AC XY: 1AN XY: 74376
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at