chr8-141151638-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001352890.3(DENND3):c.875C>T(p.Thr292Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 1,613,848 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001352890.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DENND3 | NM_001352890.3 | c.875C>T | p.Thr292Met | missense_variant | 7/23 | ENST00000519811.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DENND3 | ENST00000519811.6 | c.875C>T | p.Thr292Met | missense_variant | 7/23 | 5 | NM_001352890.3 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151976Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251404Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135884
GnomAD4 exome AF: 0.0000328 AC: 48AN: 1461872Hom.: 0 Cov.: 33 AF XY: 0.0000358 AC XY: 26AN XY: 727238
GnomAD4 genome AF: 0.0000263 AC: 4AN: 151976Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74218
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 16, 2021 | The c.635C>T (p.T212M) alteration is located in exon 7 (coding exon 6) of the DENND3 gene. This alteration results from a C to T substitution at nucleotide position 635, causing the threonine (T) at amino acid position 212 to be replaced by a methionine (M). 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