chr6-43450804-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_023932.4(DLK2):c.887G>A(p.Arg296Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000861 in 1,614,088 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R296W) has been classified as Uncertain significance.
Frequency
Consequence
NM_023932.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DLK2 | NM_023932.4 | c.887G>A | p.Arg296Gln | missense_variant | Exon 6 of 6 | ENST00000372488.8 | NP_076421.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DLK2 | ENST00000372488.8 | c.887G>A | p.Arg296Gln | missense_variant | Exon 6 of 6 | 1 | NM_023932.4 | ENSP00000361566.3 | ||
DLK2 | ENST00000357338.3 | c.887G>A | p.Arg296Gln | missense_variant | Exon 6 of 6 | 2 | ENSP00000349893.3 | |||
DLK2 | ENST00000372485.5 | c.869G>A | p.Arg290Gln | missense_variant | Exon 6 of 6 | 5 | ENSP00000361563.1 | |||
DLK2 | ENST00000430324.5 | c.602G>A | p.Arg201Gln | missense_variant | Exon 3 of 3 | 2 | ENSP00000399829.1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000152 AC: 38AN: 250806Hom.: 1 AF XY: 0.000140 AC XY: 19AN XY: 135600
GnomAD4 exome AF: 0.0000876 AC: 128AN: 1461870Hom.: 1 Cov.: 31 AF XY: 0.000100 AC XY: 73AN XY: 727236
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.887G>A (p.R296Q) alteration is located in exon 6 (coding exon 5) of the DLK2 gene. This alteration results from a G to A substitution at nucleotide position 887, causing the arginine (R) at amino acid position 296 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at