chr1-205843751-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_152491.5(PM20D1):c.743T>C(p.Met248Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00358 in 1,614,138 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_152491.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PM20D1 | NM_152491.5 | c.743T>C | p.Met248Thr | missense_variant | 6/13 | ENST00000367136.5 | |
PM20D1 | NR_135186.2 | n.803T>C | non_coding_transcript_exon_variant | 6/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PM20D1 | ENST00000367136.5 | c.743T>C | p.Met248Thr | missense_variant | 6/13 | 1 | NM_152491.5 | P1 | |
PM20D1-AS1 | ENST00000656763.1 | n.264+30166A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00252 AC: 383AN: 152184Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00271 AC: 681AN: 251380Hom.: 2 AF XY: 0.00274 AC XY: 372AN XY: 135868
GnomAD4 exome AF: 0.00369 AC: 5399AN: 1461836Hom.: 9 Cov.: 31 AF XY: 0.00364 AC XY: 2646AN XY: 727218
GnomAD4 genome ? AF: 0.00251 AC: 383AN: 152302Hom.: 2 Cov.: 32 AF XY: 0.00234 AC XY: 174AN XY: 74478
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 05, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at