3-131468100-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_007208.4(MRPL3):c.885C>T(p.Cys295Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000297 in 1,552,726 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_007208.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MRPL3 | ENST00000264995.8 | c.885C>T | p.Cys295Cys | synonymous_variant | Exon 9 of 10 | 1 | NM_007208.4 | ENSP00000264995.2 | ||
MRPL3 | ENST00000425847.6 | c.966C>T | p.Cys322Cys | synonymous_variant | Exon 10 of 11 | 2 | ENSP00000398536.2 | |||
MRPL3 | ENST00000511168.5 | c.927C>T | p.Cys309Cys | synonymous_variant | Exon 9 of 10 | 2 | ENSP00000424107.1 | |||
MRPL3 | ENST00000510043.1 | n.309C>T | non_coding_transcript_exon_variant | Exon 3 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000133 AC: 20AN: 150404Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000188 AC: 40AN: 213192Hom.: 0 AF XY: 0.000224 AC XY: 26AN XY: 116182
GnomAD4 exome AF: 0.000314 AC: 441AN: 1402252Hom.: 0 Cov.: 27 AF XY: 0.000328 AC XY: 229AN XY: 698136
GnomAD4 genome AF: 0.000133 AC: 20AN: 150474Hom.: 0 Cov.: 32 AF XY: 0.0000954 AC XY: 7AN XY: 73342
ClinVar
Submissions by phenotype
not provided Benign:2
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MRPL3-related disorder Benign:1
This variant is classified as likely 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