rs874628
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000599612.3(MPV17L2):āc.214A>Gā(p.Met72Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 1,613,910 control chromosomes in the GnomAD database, including 59,626 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
ENST00000599612.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MPV17L2 | NM_032683.3 | c.214A>G | p.Met72Val | missense_variant | 2/5 | ENST00000599612.3 | NP_116072.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MPV17L2 | ENST00000599612.3 | c.214A>G | p.Met72Val | missense_variant | 2/5 | 1 | NM_032683.3 | ENSP00000469836 | P1 | |
MPV17L2 | ENST00000532896.5 | n.659A>G | non_coding_transcript_exon_variant | 1/3 | 2 | |||||
MPV17L2 | ENST00000533807.3 | n.641A>G | non_coding_transcript_exon_variant | 1/4 | 2 | |||||
MPV17L2 | ENST00000534421.1 | n.278A>G | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.242 AC: 36844AN: 151948Hom.: 4585 Cov.: 32
GnomAD3 exomes AF: 0.237 AC: 59033AN: 249464Hom.: 7625 AF XY: 0.242 AC XY: 32746AN XY: 135332
GnomAD4 exome AF: 0.270 AC: 394680AN: 1461844Hom.: 55040 Cov.: 36 AF XY: 0.269 AC XY: 195965AN XY: 727222
GnomAD4 genome AF: 0.242 AC: 36856AN: 152066Hom.: 4586 Cov.: 32 AF XY: 0.240 AC XY: 17831AN XY: 74346
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 10, 2019 | This variant is associated with the following publications: (PMID: 21833088, 29083408) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at