8-13499310-T-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_182643.3(DLC1):āc.762A>Cā(p.Gln254His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.904 in 1,613,842 control chromosomes in the GnomAD database, including 664,991 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_182643.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLC1 | NM_182643.3 | c.762A>C | p.Gln254His | missense_variant | 2/18 | ENST00000276297.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLC1 | ENST00000276297.9 | c.762A>C | p.Gln254His | missense_variant | 2/18 | 1 | NM_182643.3 | ||
DLC1 | ENST00000511869.1 | c.762A>C | p.Gln254His | missense_variant | 2/5 | 1 | |||
DLC1 | ENST00000316609.9 | c.762A>C | p.Gln254His | missense_variant | 2/6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.847 AC: 128661AN: 151988Hom.: 55403 Cov.: 33
GnomAD3 exomes AF: 0.850 AC: 213377AN: 251074Hom.: 92585 AF XY: 0.861 AC XY: 116874AN XY: 135690
GnomAD4 exome AF: 0.910 AC: 1330008AN: 1461736Hom.: 609555 Cov.: 77 AF XY: 0.910 AC XY: 661591AN XY: 727162
GnomAD4 genome AF: 0.846 AC: 128746AN: 152106Hom.: 55436 Cov.: 33 AF XY: 0.843 AC XY: 62677AN XY: 74376
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 19, 2019 | This variant is associated with the following publications: (PMID: 26095787) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at