chr3-131462789-T-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_007208.4(MRPL3):āc.981A>Gā(p.Glu327Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,613,110 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 (ā ).
Frequency
Consequence
NM_007208.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MRPL3 | ENST00000264995.8 | c.981A>G | p.Glu327Glu | synonymous_variant | Exon 10 of 10 | 1 | NM_007208.4 | ENSP00000264995.2 | ||
MRPL3 | ENST00000425847.6 | c.1062A>G | p.Glu354Glu | synonymous_variant | Exon 11 of 11 | 2 | ENSP00000398536.2 | |||
MRPL3 | ENST00000511168.5 | c.1023A>G | p.Glu341Glu | synonymous_variant | Exon 10 of 10 | 2 | ENSP00000424107.1 | |||
MRPL3 | ENST00000510043.1 | n.405A>G | non_coding_transcript_exon_variant | Exon 4 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250488Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135356
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1460988Hom.: 0 Cov.: 30 AF XY: 0.00000688 AC XY: 5AN XY: 726802
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74310
ClinVar
Submissions by phenotype
not provided Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at