1-205832628-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_152491.5(PM20D1):c.1255G>A(p.Val419Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00975 in 1,614,070 control chromosomes in the GnomAD database, including 93 homozygotes. 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 Benign (★).
Frequency
Genomes: 𝑓 0.0079 ( 9 hom., cov: 32)
Exomes 𝑓: 0.0099 ( 84 hom. )
Consequence
PM20D1
NM_152491.5 missense
NM_152491.5 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: 1.10
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.004850149).
BP6
?
Variant 1-205832628-C-T is Benign according to our data. Variant chr1-205832628-C-T is described in ClinVar as [Benign]. Clinvar id is 717694.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PM20D1 | NM_152491.5 | c.1255G>A | p.Val419Ile | missense_variant | 11/13 | ENST00000367136.5 | |
PM20D1 | NR_135186.2 | n.1253G>A | non_coding_transcript_exon_variant | 10/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PM20D1 | ENST00000367136.5 | c.1255G>A | p.Val419Ile | missense_variant | 11/13 | 1 | NM_152491.5 | P1 | |
PM20D1-AS1 | ENST00000656763.1 | n.264+19043C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00791 AC: 1204AN: 152134Hom.: 9 Cov.: 32
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00775 AC: 1948AN: 251334Hom.: 15 AF XY: 0.00757 AC XY: 1028AN XY: 135838
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GnomAD4 exome AF: 0.00994 AC: 14534AN: 1461818Hom.: 84 Cov.: 30 AF XY: 0.00983 AC XY: 7152AN XY: 727210
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GnomAD4 genome ? AF: 0.00790 AC: 1203AN: 152252Hom.: 9 Cov.: 32 AF XY: 0.00752 AC XY: 560AN XY: 74466
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102
ExAC
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955
Asia WGS
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 26, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at