17-2033556-A-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001383.6(DPH1):c.113A>C(p.Lys38Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000465 in 1,614,204 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. K38K) has been classified as Likely benign.
Frequency
Consequence
NM_001383.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DPH1 | NM_001383.6 | c.113A>C | p.Lys38Thr | missense_variant | 2/13 | ENST00000263083.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DPH1 | ENST00000263083.12 | c.113A>C | p.Lys38Thr | missense_variant | 2/13 | 1 | NM_001383.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000268 AC: 67AN: 249552Hom.: 0 AF XY: 0.000214 AC XY: 29AN XY: 135400
GnomAD4 exome AF: 0.0000438 AC: 64AN: 1461868Hom.: 0 Cov.: 32 AF XY: 0.0000413 AC XY: 30AN XY: 727230
GnomAD4 genome ? AF: 0.0000722 AC: 11AN: 152336Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74494
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at