rs1059276
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005588.3(MEP1A):c.*167C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 540,010 control chromosomes in the GnomAD database, including 105,411 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.63 ( 30437 hom., cov: 29)
Exomes 𝑓: 0.62 ( 74974 hom. )
Consequence
MEP1A
NM_005588.3 3_prime_UTR
NM_005588.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.131
Genes affected
MEP1A (HGNC:7015): (meprin A subunit alpha) Predicted to enable metalloendopeptidase activity. Predicted to be involved in proteolysis. Located in extracellular exosome. Part of meprin A complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MEP1A | NM_005588.3 | c.*167C>A | 3_prime_UTR_variant | 14/14 | ENST00000230588.9 | ||
MEP1A | XM_011514628.2 | c.*167C>A | 3_prime_UTR_variant | 13/13 | |||
MEP1A | XM_011514629.3 | c.2084+3754C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MEP1A | ENST00000230588.9 | c.*167C>A | 3_prime_UTR_variant | 14/14 | 1 | NM_005588.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.631 AC: 95366AN: 151074Hom.: 30398 Cov.: 29
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GnomAD4 exome AF: 0.618 AC: 240101AN: 388820Hom.: 74974 Cov.: 5 AF XY: 0.622 AC XY: 125221AN XY: 201370
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GnomAD4 genome ? AF: 0.631 AC: 95455AN: 151190Hom.: 30437 Cov.: 29 AF XY: 0.629 AC XY: 46455AN XY: 73800
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at