5-60603522-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018369.3(DEPDC1B):c.1111G>A(p.Val371Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000932 in 1,608,856 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_018369.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DEPDC1B | NM_018369.3 | c.1111G>A | p.Val371Met | missense_variant | Exon 9 of 11 | ENST00000265036.10 | NP_060839.2 | |
DEPDC1B | NM_001145208.2 | c.1111G>A | p.Val371Met | missense_variant | Exon 9 of 10 | NP_001138680.1 | ||
DEPDC1B | XM_011543509.3 | c.1066G>A | p.Val356Met | missense_variant | Exon 9 of 11 | XP_011541811.1 | ||
DEPDC1B | XM_047417369.1 | c.1066G>A | p.Val356Met | missense_variant | Exon 9 of 10 | XP_047273325.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DEPDC1B | ENST00000265036.10 | c.1111G>A | p.Val371Met | missense_variant | Exon 9 of 11 | 1 | NM_018369.3 | ENSP00000265036.5 | ||
DEPDC1B | ENST00000453022.6 | c.1111G>A | p.Val371Met | missense_variant | Exon 9 of 10 | 2 | ENSP00000389101.2 | |||
DEPDC1B | ENST00000512078.5 | n.*1108G>A | non_coding_transcript_exon_variant | Exon 10 of 11 | 2 | ENSP00000427527.1 | ||||
DEPDC1B | ENST00000512078.5 | n.*1108G>A | 3_prime_UTR_variant | Exon 10 of 11 | 2 | ENSP00000427527.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152092Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000327 AC: 8AN: 244670Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132172
GnomAD4 exome AF: 0.00000961 AC: 14AN: 1456646Hom.: 0 Cov.: 30 AF XY: 0.00000828 AC XY: 6AN XY: 724568
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74416
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1111G>A (p.V371M) alteration is located in exon 9 (coding exon 9) of the DEPDC1B gene. This alteration results from a G to A substitution at nucleotide position 1111, causing the valine (V) at amino acid position 371 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