chr4-154236578-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001358235.2(DCHS2):c.8074C>T(p.Arg2692Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000777 in 1,613,936 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/16 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
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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 |
---|---|---|---|---|---|---|---|
DCHS2 | NM_001358235.2 | c.8074C>T | p.Arg2692Cys | missense_variant | 20/20 | ENST00000357232.10 | |
LOC101927947 | XR_007058336.1 | n.4255+29525G>A | intron_variant, non_coding_transcript_variant | ||||
LOC101927947 | XR_007058335.1 | n.689+29525G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCHS2 | ENST00000357232.10 | c.8074C>T | p.Arg2692Cys | missense_variant | 20/20 | 1 | NM_001358235.2 | P1 | |
ENST00000625026.1 | n.599G>A | non_coding_transcript_exon_variant | 1/1 | ||||||
ENST00000660197.1 | n.412+29525G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00404 AC: 614AN: 152134Hom.: 9 Cov.: 33
GnomAD3 exomes AF: 0.00112 AC: 282AN: 250800Hom.: 2 AF XY: 0.000760 AC XY: 103AN XY: 135510
GnomAD4 exome AF: 0.000434 AC: 634AN: 1461684Hom.: 2 Cov.: 34 AF XY: 0.000380 AC XY: 276AN XY: 727136
GnomAD4 genome ? AF: 0.00407 AC: 620AN: 152252Hom.: 9 Cov.: 33 AF XY: 0.00391 AC XY: 291AN XY: 74444
ClinVar
Submissions by phenotype
DCHS2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 19, 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