4-154236252-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_001358235.2(DCHS2):c.8400G>A(p.Pro2800Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00135 in 1,613,936 control chromosomes in the GnomAD database, including 24 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 synonymous
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DCHS2 | NM_001358235.2 | c.8400G>A | p.Pro2800Pro | synonymous_variant | Exon 20 of 20 | ENST00000357232.10 | NP_001345164.1 | |
LOC101927947 | XR_007058335.1 | n.689+29199C>T | intron_variant | Intron 5 of 5 | ||||
LOC101927947 | XR_007058336.1 | n.4255+29199C>T | intron_variant | Intron 12 of 14 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00669 AC: 1017AN: 152098Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00185 AC: 463AN: 250340Hom.: 6 AF XY: 0.00141 AC XY: 191AN XY: 135272
GnomAD4 exome AF: 0.000787 AC: 1151AN: 1461720Hom.: 14 Cov.: 34 AF XY: 0.000694 AC XY: 505AN XY: 727170
GnomAD4 genome AF: 0.00673 AC: 1024AN: 152216Hom.: 10 Cov.: 32 AF XY: 0.00656 AC XY: 488AN XY: 74410
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