1-205841842-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000367136.5(PM20D1):c.1013C>A(p.Thr338Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000115 in 1,570,030 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000367136.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PM20D1 | NM_152491.5 | c.1013C>A | p.Thr338Lys | missense_variant | 9/13 | ENST00000367136.5 | NP_689704.4 | |
PM20D1 | NR_135186.2 | n.1011C>A | non_coding_transcript_exon_variant | 8/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PM20D1 | ENST00000367136.5 | c.1013C>A | p.Thr338Lys | missense_variant | 9/13 | 1 | NM_152491.5 | ENSP00000356104 | P1 | |
PM20D1-AS1 | ENST00000656763.1 | n.264+28257G>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000640 AC: 12AN: 187586Hom.: 0 AF XY: 0.0000402 AC XY: 4AN XY: 99570
GnomAD4 exome AF: 0.0000106 AC: 15AN: 1417914Hom.: 0 Cov.: 31 AF XY: 0.00000856 AC XY: 6AN XY: 701050
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152116Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 01, 2022 | The c.1013C>A (p.T338K) alteration is located in exon 9 (coding exon 9) of the PM20D1 gene. This alteration results from a C to A substitution at nucleotide position 1013, causing the threonine (T) at amino acid position 338 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at