chr17-47827054-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_145255.4(MRPL10):c.373G>A(p.Val125Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 1,611,434 control chromosomes in the GnomAD database, including 102,695 homozygotes. 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 Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_145255.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRPL10 | NM_145255.4 | c.373G>A | p.Val125Ile | missense_variant | 3/5 | ENST00000351111.7 | |
MRPL10 | NM_148887.3 | c.403G>A | p.Val135Ile | missense_variant | 4/6 | ||
MRPL10 | XM_024450575.2 | c.403G>A | p.Val135Ile | missense_variant | 4/6 | ||
MRPL10 | NR_037575.2 | n.552G>A | non_coding_transcript_exon_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRPL10 | ENST00000351111.7 | c.373G>A | p.Val125Ile | missense_variant | 3/5 | 1 | NM_145255.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.271 AC: 41240AN: 152004Hom.: 6939 Cov.: 32
GnomAD3 exomes AF: 0.286 AC: 71215AN: 248826Hom.: 12200 AF XY: 0.294 AC XY: 39528AN XY: 134440
GnomAD4 exome AF: 0.351 AC: 511891AN: 1459312Hom.: 95754 Cov.: 39 AF XY: 0.348 AC XY: 252627AN XY: 725866
GnomAD4 genome AF: 0.271 AC: 41259AN: 152122Hom.: 6941 Cov.: 32 AF XY: 0.269 AC XY: 20040AN XY: 74372
ClinVar
Submissions by phenotype
MRPL10-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at