chr7-42932454-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_031903.3(MRPL32):c.68A>G(p.Tyr23Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000806 in 1,611,982 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_031903.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRPL32 | NM_031903.3 | c.68A>G | p.Tyr23Cys | missense_variant | 1/3 | ENST00000223324.3 | |
MRPL32 | NR_156497.1 | n.79A>G | non_coding_transcript_exon_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRPL32 | ENST00000223324.3 | c.68A>G | p.Tyr23Cys | missense_variant | 1/3 | 1 | NM_031903.3 | P1 | |
MRPL32 | ENST00000432845.1 | c.68A>G | p.Tyr23Cys | missense_variant, NMD_transcript_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151666Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000480 AC: 12AN: 249980Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135330
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1460316Hom.: 0 Cov.: 32 AF XY: 0.00000964 AC XY: 7AN XY: 726112
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151666Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74052
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 17, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at