chr8-10054643-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_012331.5(MSRA):āc.127C>Gā(p.Gln43Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000165 in 1,571,180 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 (ā ).
Frequency
Consequence
NM_012331.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MSRA | NM_012331.5 | c.127C>G | p.Gln43Glu | missense_variant | 1/6 | ENST00000317173.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MSRA | ENST00000317173.9 | c.127C>G | p.Gln43Glu | missense_variant | 1/6 | 1 | NM_012331.5 | P1 | |
ENST00000659604.1 | n.116+283G>C | intron_variant, non_coding_transcript_variant | |||||||
MSRA | ENST00000518255.5 | c.127C>G | p.Gln43Glu | missense_variant | 1/6 | 5 | |||
MSRA | ENST00000441698.6 | c.127C>G | p.Gln43Glu | missense_variant | 1/5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152014Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000237 AC: 5AN: 211224Hom.: 0 AF XY: 0.00000861 AC XY: 1AN XY: 116136
GnomAD4 exome AF: 0.0000176 AC: 25AN: 1419166Hom.: 0 Cov.: 32 AF XY: 0.0000184 AC XY: 13AN XY: 705932
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152014Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74246
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2023 | The c.127C>G (p.Q43E) alteration is located in exon 1 (coding exon 1) of the MSRA gene. This alteration results from a C to G substitution at nucleotide position 127, causing the glutamine (Q) at amino acid position 43 to be replaced by a glutamic acid (E). 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