3-131462839-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_007208.4(MRPL3):c.931G>A(p.Gly311Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00333 in 1,611,402 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_007208.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MRPL3 | NM_007208.4 | c.931G>A | p.Gly311Ser | missense_variant | 10/10 | ENST00000264995.8 | NP_009139.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MRPL3 | ENST00000264995.8 | c.931G>A | p.Gly311Ser | missense_variant | 10/10 | 1 | NM_007208.4 | ENSP00000264995 | P1 | |
MRPL3 | ENST00000425847.6 | c.1012G>A | p.Gly338Ser | missense_variant | 11/11 | 2 | ENSP00000398536 | |||
MRPL3 | ENST00000511168.5 | c.976G>A | p.Gly326Ser | missense_variant | 10/10 | 2 | ENSP00000424107 | |||
MRPL3 | ENST00000510043.1 | n.355G>A | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00314 AC: 477AN: 152002Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00368 AC: 920AN: 249772Hom.: 7 AF XY: 0.00416 AC XY: 561AN XY: 134998
GnomAD4 exome AF: 0.00335 AC: 4894AN: 1459282Hom.: 20 Cov.: 30 AF XY: 0.00354 AC XY: 2571AN XY: 725978
GnomAD4 genome AF: 0.00312 AC: 475AN: 152120Hom.: 3 Cov.: 32 AF XY: 0.00313 AC XY: 233AN XY: 74352
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:5
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Oct 13, 2016 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Feb 23, 2016 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2024 | MRPL3: BP4, BS2 - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 11, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 24, 2024 | - - |
MRPL3-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 13, 2024 | 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