rs17348507
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152491.5(PM20D1):c.257-50T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0478 in 1,491,854 control chromosomes in the GnomAD database, including 1,956 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 0.053 ( 285 hom., cov: 32)
Exomes 𝑓: 0.047 ( 1671 hom. )
Consequence
PM20D1
NM_152491.5 intron
NM_152491.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.665
Genes affected
PM20D1 (HGNC:26518): (peptidase M20 domain containing 1) Enables hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides. Involved in several processes, including amide biosynthetic process; cellular amide catabolic process; and negative regulation of neuron death. Located in extracellular exosome. [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=-0.77).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0837 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PM20D1 | NM_152491.5 | c.257-50T>C | intron_variant | ENST00000367136.5 | |||
PM20D1 | NR_135186.2 | n.317-50T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PM20D1 | ENST00000367136.5 | c.257-50T>C | intron_variant | 1 | NM_152491.5 | P1 | |||
PM20D1-AS1 | ENST00000656763.1 | n.264+32022A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0534 AC: 8127AN: 152162Hom.: 286 Cov.: 32
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GnomAD3 exomes AF: 0.0413 AC: 9601AN: 232434Hom.: 263 AF XY: 0.0427 AC XY: 5379AN XY: 125884
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GnomAD4 exome AF: 0.0472 AC: 63162AN: 1339572Hom.: 1671 Cov.: 21 AF XY: 0.0476 AC XY: 31803AN XY: 668554
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GnomAD4 genome ? AF: 0.0534 AC: 8137AN: 152282Hom.: 285 Cov.: 32 AF XY: 0.0521 AC XY: 3876AN XY: 74456
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ClinVar
Not reported inComputational scores
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Name
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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