7-140523418-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_015689.5(DENND2A):c.2554G>A(p.Asp852Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000805 in 1,613,960 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_015689.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DENND2A | NM_015689.5 | c.2554G>A | p.Asp852Asn | missense_variant | Exon 17 of 20 | ENST00000496613.6 | NP_056504.3 | |
DENND2A | NM_001318052.2 | c.2554G>A | p.Asp852Asn | missense_variant | Exon 16 of 19 | NP_001304981.1 | ||
DENND2A | NM_001362678.2 | c.2554G>A | p.Asp852Asn | missense_variant | Exon 17 of 20 | NP_001349607.1 | ||
DENND2A | NR_134477.1 | n.2641G>A | non_coding_transcript_exon_variant | Exon 15 of 18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DENND2A | ENST00000496613.6 | c.2554G>A | p.Asp852Asn | missense_variant | Exon 17 of 20 | 2 | NM_015689.5 | ENSP00000419654.1 | ||
DENND2A | ENST00000275884.10 | c.2554G>A | p.Asp852Asn | missense_variant | Exon 16 of 19 | 1 | ENSP00000275884.6 | |||
DENND2A | ENST00000537639.5 | c.2554G>A | p.Asp852Asn | missense_variant | Exon 15 of 18 | 1 | ENSP00000442245.1 | |||
DENND2A | ENST00000461883.5 | n.2496G>A | non_coding_transcript_exon_variant | Exon 15 of 18 | 1 | ENSP00000417673.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152172Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461788Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727192
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2554G>A (p.D852N) alteration is located in exon 15 (coding exon 15) of the DENND2A gene. This alteration results from a G to A substitution at nucleotide position 2554, causing the aspartic acid (D) at amino acid position 852 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