3-131462785-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP6
The NM_007208.4(MRPL3):c.985C>T(p.Pro329Ser) variant causes a missense change. The variant allele was found at a frequency of 0.000169 in 1,612,932 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_007208.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MRPL3 | ENST00000264995.8 | c.985C>T | p.Pro329Ser | missense_variant | Exon 10 of 10 | 1 | NM_007208.4 | ENSP00000264995.2 | ||
MRPL3 | ENST00000425847.6 | c.1066C>T | p.Pro356Ser | missense_variant | Exon 11 of 11 | 2 | ENSP00000398536.2 | |||
MRPL3 | ENST00000511168.5 | c.1027C>T | p.Pro343Ser | missense_variant | Exon 10 of 10 | 2 | ENSP00000424107.1 | |||
MRPL3 | ENST00000510043.1 | n.409C>T | non_coding_transcript_exon_variant | Exon 4 of 4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000191 AC: 29AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000319 AC: 80AN: 250402Hom.: 0 AF XY: 0.000370 AC XY: 50AN XY: 135292
GnomAD4 exome AF: 0.000167 AC: 244AN: 1460814Hom.: 1 Cov.: 30 AF XY: 0.000183 AC XY: 133AN XY: 726698
GnomAD4 genome AF: 0.000191 AC: 29AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.000162 AC XY: 12AN XY: 74300
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
- -
Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function -
not specified Uncertain:1
The c.985C>T (p.P329S) alteration is located in exon 10 (coding exon 10) of the MRPL3 gene. This alteration results from a C to T substitution at nucleotide position 985, causing the proline (P) at amino acid position 329 to be replaced by a serine (S). 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