6-43450909-T-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_023932.4(DLK2):c.782A>T(p.Asp261Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000148 in 1,614,110 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_023932.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DLK2 | NM_023932.4 | c.782A>T | p.Asp261Val | missense_variant | 6/6 | ENST00000372488.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DLK2 | ENST00000372488.8 | c.782A>T | p.Asp261Val | missense_variant | 6/6 | 1 | NM_023932.4 | P4 | |
DLK2 | ENST00000357338.3 | c.782A>T | p.Asp261Val | missense_variant | 6/6 | 2 | P4 | ||
DLK2 | ENST00000372485.5 | c.764A>T | p.Asp255Val | missense_variant | 6/6 | 5 | A1 | ||
DLK2 | ENST00000430324.5 | c.500A>T | p.Asp167Val | missense_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000315 AC: 48AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000999 AC: 25AN: 250334Hom.: 0 AF XY: 0.0000812 AC XY: 11AN XY: 135442
GnomAD4 exome AF: 0.000131 AC: 191AN: 1461846Hom.: 0 Cov.: 31 AF XY: 0.000127 AC XY: 92AN XY: 727224
GnomAD4 genome AF: 0.000315 AC: 48AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.000363 AC XY: 27AN XY: 74446
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | DLK2: BP4 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at