rs17373860
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001358235.2(DCHS2):c.625C>T(p.Pro209Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0692 in 1,551,632 control chromosomes in the GnomAD database, including 4,412 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001358235.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCHS2 | NM_001358235.2 | c.625C>T | p.Pro209Ser | missense_variant | 1/20 | ENST00000357232.10 | |
DCHS2 | NM_001142552.2 | c.625C>T | p.Pro209Ser | missense_variant | 1/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCHS2 | ENST00000357232.10 | c.625C>T | p.Pro209Ser | missense_variant | 1/20 | 1 | NM_001358235.2 | P1 | |
DCHS2 | ENST00000339452.2 | c.625C>T | p.Pro209Ser | missense_variant | 1/8 | 1 | |||
DCHS2 | ENST00000456341.2 | n.604C>T | non_coding_transcript_exon_variant | 1/2 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0581 AC: 8836AN: 152212Hom.: 407 Cov.: 33
GnomAD3 exomes AF: 0.0690 AC: 10577AN: 153180Hom.: 557 AF XY: 0.0658 AC XY: 5358AN XY: 81438
GnomAD4 exome AF: 0.0704 AC: 98531AN: 1399302Hom.: 4005 Cov.: 92 AF XY: 0.0692 AC XY: 47769AN XY: 690170
GnomAD4 genome ? AF: 0.0581 AC: 8849AN: 152330Hom.: 407 Cov.: 33 AF XY: 0.0598 AC XY: 4452AN XY: 74486
ClinVar
Submissions by phenotype
DCHS2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 01, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at