chr7-140527473-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_015689.5(DENND2A):c.2350G>A(p.Ala784Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000661 in 1,604,652 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A784E) 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 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DENND2A | NM_015689.5 | c.2350G>A | p.Ala784Thr | missense_variant | 15/20 | ENST00000496613.6 | |
DENND2A | NM_001318052.2 | c.2350G>A | p.Ala784Thr | missense_variant | 14/19 | ||
DENND2A | NM_001362678.2 | c.2350G>A | p.Ala784Thr | missense_variant | 15/20 | ||
DENND2A | NR_134477.1 | n.2473-36G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DENND2A | ENST00000496613.6 | c.2350G>A | p.Ala784Thr | missense_variant | 15/20 | 2 | NM_015689.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000214 AC: 5AN: 233374Hom.: 0 AF XY: 0.00000784 AC XY: 1AN XY: 127490
GnomAD4 exome AF: 0.0000702 AC: 102AN: 1452534Hom.: 0 Cov.: 31 AF XY: 0.0000582 AC XY: 42AN XY: 721476
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2024 | The c.2350G>A (p.A784T) alteration is located in exon 13 (coding exon 13) of the DENND2A gene. This alteration results from a G to A substitution at nucleotide position 2350, causing the alanine (A) at amino acid position 784 to be replaced by a threonine (T). 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