chr6-43451036-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_023932.4(DLK2):c.655C>T(p.Arg219Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000434 in 1,614,094 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_023932.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DLK2 | NM_023932.4 | c.655C>T | p.Arg219Cys | 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.655C>T | p.Arg219Cys | missense_variant | Exon 6 of 6 | 1 | NM_023932.4 | ENSP00000361566.3 | ||
DLK2 | ENST00000357338.3 | c.655C>T | p.Arg219Cys | missense_variant | Exon 6 of 6 | 2 | ENSP00000349893.3 | |||
DLK2 | ENST00000372485.5 | c.637C>T | p.Arg213Cys | missense_variant | Exon 6 of 6 | 5 | ENSP00000361563.1 | |||
DLK2 | ENST00000430324.5 | c.370C>T | p.Arg124Cys | missense_variant | Exon 3 of 3 | 2 | ENSP00000399829.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152226Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251184Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135814
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461868Hom.: 0 Cov.: 33 AF XY: 0.00000413 AC XY: 3AN XY: 727232
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152226Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74372
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.655C>T (p.R219C) alteration is located in exon 6 (coding exon 5) of the DLK2 gene. This alteration results from a C to T substitution at nucleotide position 655, causing the arginine (R) at amino acid position 219 to be replaced by a cysteine (C). 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