1-114600307-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001256404.2(DENND2C):c.2002G>A(p.Asp668Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,848 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
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DENND2C | ENST00000393274.6 | c.2002G>A | p.Asp668Asn | missense_variant | Exon 15 of 21 | 5 | NM_001256404.2 | ENSP00000376955.1 | ||
DENND2C | ENST00000481894.1 | n.1290G>A | non_coding_transcript_exon_variant | Exon 12 of 18 | 1 | |||||
DENND2C | ENST00000393276.7 | c.1831G>A | p.Asp611Asn | missense_variant | Exon 12 of 18 | 5 | ENSP00000376957.3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251412Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135870
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461848Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727224
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1831G>A (p.D611N) 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 1831, causing the aspartic acid (D) at amino acid position 611 to be replaced by an asparagine (N). 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