rs3816747
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_182643.3(DLC1):c.779C>T(p.Thr260Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.916 in 1,614,014 control chromosomes in the GnomAD database, including 680,659 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 (★★). 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 -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLC1 | NM_182643.3 | c.779C>T | p.Thr260Ile | missense_variant | 2/18 | ENST00000276297.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLC1 | ENST00000276297.9 | c.779C>T | p.Thr260Ile | missense_variant | 2/18 | 1 | NM_182643.3 | ||
DLC1 | ENST00000511869.1 | c.779C>T | p.Thr260Ile | missense_variant | 2/5 | 1 | |||
DLC1 | ENST00000316609.9 | c.779C>T | p.Thr260Ile | missense_variant | 2/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.888 AC: 135081AN: 152128Hom.: 60458 Cov.: 33
GnomAD3 exomes AF: 0.869 AC: 218119AN: 251102Hom.: 96536 AF XY: 0.880 AC XY: 119424AN XY: 135706
GnomAD4 exome AF: 0.918 AC: 1342592AN: 1461768Hom.: 620158 Cov.: 69 AF XY: 0.920 AC XY: 668779AN XY: 727194
GnomAD4 genome ? AF: 0.888 AC: 135182AN: 152246Hom.: 60501 Cov.: 33 AF XY: 0.884 AC XY: 65787AN XY: 74430
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
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