4-154236809-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001358235.2(DCHS2):c.7843G>A(p.Gly2615Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00173 in 1,613,958 control chromosomes in the GnomAD database, including 45 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001358235.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DCHS2 | NM_001358235.2 | c.7843G>A | p.Gly2615Ser | missense_variant | Exon 20 of 20 | ENST00000357232.10 | NP_001345164.1 | |
LOC101927947 | XR_007058335.1 | n.689+29756C>T | intron_variant | Intron 5 of 5 | ||||
LOC101927947 | XR_007058336.1 | n.4255+29756C>T | intron_variant | Intron 12 of 14 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00920 AC: 1400AN: 152148Hom.: 25 Cov.: 33
GnomAD3 exomes AF: 0.00231 AC: 578AN: 250334Hom.: 10 AF XY: 0.00177 AC XY: 239AN XY: 135276
GnomAD4 exome AF: 0.000948 AC: 1386AN: 1461692Hom.: 20 Cov.: 34 AF XY: 0.000825 AC XY: 600AN XY: 727152
GnomAD4 genome AF: 0.00921 AC: 1402AN: 152266Hom.: 25 Cov.: 33 AF XY: 0.00892 AC XY: 664AN XY: 74460
ClinVar
Submissions by phenotype
DCHS2-related disorder Benign:1
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