1-68496987-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001114120.3(DEPDC1):c.13G>T(p.Gly5Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,344 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_001114120.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DEPDC1 | NM_001114120.3 | c.13G>T | p.Gly5Cys | missense_variant | Exon 1 of 12 | ENST00000456315.7 | NP_001107592.1 | |
DEPDC1 | NM_017779.6 | c.13G>T | p.Gly5Cys | missense_variant | Exon 1 of 11 | NP_060249.2 | ||
DEPDC1-AS1 | NR_110671.1 | n.96+216C>A | intron_variant | Intron 1 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DEPDC1 | ENST00000456315.7 | c.13G>T | p.Gly5Cys | missense_variant | Exon 1 of 12 | 1 | NM_001114120.3 | ENSP00000412292.2 | ||
DEPDC1 | ENST00000370966.9 | c.13G>T | p.Gly5Cys | missense_variant | Exon 1 of 11 | 1 | ENSP00000360005.5 | |||
DEPDC1-AS1 | ENST00000428732.1 | n.96+216C>A | intron_variant | Intron 1 of 2 | 1 | |||||
DEPDC1 | ENST00000525124.1 | c.-385G>T | 5_prime_UTR_variant | Exon 1 of 5 | 3 | ENSP00000431477.1 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000281 AC: 7AN: 249088Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134740
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461124Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 726834
GnomAD4 genome AF: 0.000112 AC: 17AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.13G>T (p.G5C) alteration is located in exon 1 (coding exon 1) of the DEPDC1 gene. This alteration results from a G to T substitution at nucleotide position 13, causing the glycine (G) at amino acid position 5 to be replaced by a cysteine (C). 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