4-77952515-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020236.4(MRPL1):c.886C>T(p.Arg296Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000353 in 1,612,678 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020236.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MRPL1 | NM_020236.4 | c.886C>T | p.Arg296Cys | missense_variant | Exon 9 of 9 | ENST00000315567.13 | NP_064621.3 | |
MRPL1 | XM_047416089.1 | c.820C>T | p.Arg274Cys | missense_variant | Exon 9 of 9 | XP_047272045.1 | ||
LOC102724916 | XR_001741744.2 | n.-5G>A | upstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MRPL1 | ENST00000315567.13 | c.886C>T | p.Arg296Cys | missense_variant | Exon 9 of 9 | 1 | NM_020236.4 | ENSP00000315017.8 | ||
MRPL1 | ENST00000502384.3 | c.663C>T | p.Phe221Phe | synonymous_variant | Exon 6 of 6 | 5 | ENSP00000421616.1 | |||
MRPL1 | ENST00000504901.2 | n.267C>T | non_coding_transcript_exon_variant | Exon 4 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152090Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000320 AC: 8AN: 250122Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135274
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1460588Hom.: 0 Cov.: 30 AF XY: 0.0000330 AC XY: 24AN XY: 726606
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152090Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74284
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.886C>T (p.R296C) alteration is located in exon 9 (coding exon 9) of the MRPL1 gene. This alteration results from a C to T substitution at nucleotide position 886, causing the arginine (R) at amino acid position 296 to be replaced by a cysteine (C). 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