chr1-114600321-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001256404.2(DENND2C):c.1988G>A(p.Arg663Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000958 in 1,461,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001256404.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DENND2C | ENST00000393274.6 | c.1988G>A | p.Arg663Gln | missense_variant | Exon 15 of 21 | 5 | NM_001256404.2 | ENSP00000376955.1 | ||
DENND2C | ENST00000481894.1 | n.1276G>A | non_coding_transcript_exon_variant | Exon 12 of 18 | 1 | |||||
DENND2C | ENST00000393276.7 | c.1817G>A | p.Arg606Gln | missense_variant | Exon 12 of 18 | 5 | ENSP00000376957.3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251386Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135850
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461832Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727210
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1817G>A (p.R606Q) alteration is located in exon 12 (coding exon 11) of the DENND2C gene. This alteration results from a G to A substitution at nucleotide position 1817, causing the arginine (R) at amino acid position 606 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