7-140525764-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015689.5(DENND2A):c.2534G>A(p.Arg845Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000162 in 1,605,820 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R845W) has been classified as Uncertain significance.
Frequency
Consequence
NM_015689.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DENND2A | NM_015689.5 | c.2534G>A | p.Arg845Gln | missense_variant | Exon 16 of 20 | ENST00000496613.6 | NP_056504.3 | |
DENND2A | NM_001318052.2 | c.2534G>A | p.Arg845Gln | missense_variant | Exon 15 of 19 | NP_001304981.1 | ||
DENND2A | NM_001362678.2 | c.2534G>A | p.Arg845Gln | missense_variant | Exon 16 of 20 | NP_001349607.1 | ||
DENND2A | NR_134477.1 | n.2621G>A | non_coding_transcript_exon_variant | Exon 14 of 18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DENND2A | ENST00000496613.6 | c.2534G>A | p.Arg845Gln | missense_variant | Exon 16 of 20 | 2 | NM_015689.5 | ENSP00000419654.1 | ||
DENND2A | ENST00000275884.10 | c.2534G>A | p.Arg845Gln | missense_variant | Exon 15 of 19 | 1 | ENSP00000275884.6 | |||
DENND2A | ENST00000537639.5 | c.2534G>A | p.Arg845Gln | missense_variant | Exon 14 of 18 | 1 | ENSP00000442245.1 | |||
DENND2A | ENST00000461883.5 | n.2476G>A | non_coding_transcript_exon_variant | Exon 14 of 18 | 1 | ENSP00000417673.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152128Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000250 AC: 6AN: 240476Hom.: 0 AF XY: 0.0000229 AC XY: 3AN XY: 130828
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1453692Hom.: 0 Cov.: 30 AF XY: 0.0000152 AC XY: 11AN XY: 722828
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152128Hom.: 0 Cov.: 31 AF XY: 0.0000538 AC XY: 4AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2534G>A (p.R845Q) alteration is located in exon 14 (coding exon 14) of the DENND2A gene. This alteration results from a G to A substitution at nucleotide position 2534, causing the arginine (R) at amino acid position 845 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