rs146411944
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_003737.4(DCHS1):c.5938A>T(p.Thr1980Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00166 in 1,612,600 control chromosomes in the GnomAD database, including 48 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. T1980T) has been classified as Likely benign.
Frequency
Consequence
NM_003737.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCHS1 | NM_003737.4 | c.5938A>T | p.Thr1980Ser | missense_variant | 14/21 | ENST00000299441.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCHS1 | ENST00000299441.5 | c.5938A>T | p.Thr1980Ser | missense_variant | 14/21 | 1 | NM_003737.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00225 AC: 342AN: 151664Hom.: 6 Cov.: 33
GnomAD3 exomes AF: 0.00595 AC: 1488AN: 250284Hom.: 32 AF XY: 0.00465 AC XY: 630AN XY: 135520
GnomAD4 exome AF: 0.00160 AC: 2331AN: 1460818Hom.: 41 Cov.: 71 AF XY: 0.00140 AC XY: 1019AN XY: 726632
GnomAD4 genome ? AF: 0.00227 AC: 344AN: 151782Hom.: 7 Cov.: 33 AF XY: 0.00213 AC XY: 158AN XY: 74200
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 09, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Feb 07, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at