rs2274658
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005588.3(MEP1A):c.1405G>T(p.Val469Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 1,613,798 control chromosomes in the GnomAD database, including 128,185 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_005588.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MEP1A | NM_005588.3 | c.1405G>T | p.Val469Leu | missense_variant | 11/14 | ENST00000230588.9 | |
MEP1A | XM_011514628.2 | c.1489G>T | p.Val497Leu | missense_variant | 10/13 | ||
MEP1A | XM_011514629.3 | c.1405G>T | p.Val469Leu | missense_variant | 11/14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MEP1A | ENST00000230588.9 | c.1405G>T | p.Val469Leu | missense_variant | 11/14 | 1 | NM_005588.3 | P1 | |
MEP1A | ENST00000611727.2 | c.1489G>T | p.Val497Leu | missense_variant | 10/13 | 1 | |||
MEP1A | ENST00000680769.1 | n.1586G>T | non_coding_transcript_exon_variant | 9/12 | |||||
MEP1A | ENST00000680229.1 | c.*590G>T | 3_prime_UTR_variant, NMD_transcript_variant | 11/14 |
Frequencies
GnomAD3 genomes ? AF: 0.423 AC: 64242AN: 151924Hom.: 13946 Cov.: 32
GnomAD3 exomes AF: 0.395 AC: 99288AN: 251458Hom.: 20444 AF XY: 0.392 AC XY: 53327AN XY: 135904
GnomAD4 exome AF: 0.392 AC: 572900AN: 1461756Hom.: 114222 Cov.: 45 AF XY: 0.392 AC XY: 285410AN XY: 727182
GnomAD4 genome ? AF: 0.423 AC: 64307AN: 152042Hom.: 13963 Cov.: 32 AF XY: 0.421 AC XY: 31295AN XY: 74308
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at