chr1-68485584-C-A

Variant names:

• chr1-68485584-C-A
• rs4926344
• NM_001114120.3:c.769+1353G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001114120.3(DEPDC1):​c.769+1353G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 151,806 control chromosomes in the GnomAD database, including 25,183 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.56 (25183 hom., cov: 31)
• Consequence: DEPDC1 NM_001114120.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.363
• Publications: 0 publications found

Genes affected

DEPDC1 (HGNC:22949): (DEP domain containing 1) Predicted to enable GTPase activator activity. Involved in negative regulation of transcription, DNA-templated. Located in nucleus. Part of transcription repressor complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DEPDC1	NM_001114120.3	c.769+1353G>T		intron_variant	Intron 6 of 11	ENST00000456315.7	NP_001107592.1
DEPDC1	NM_017779.6	c.769+1353G>T		intron_variant	Intron 6 of 10		NP_060249.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DEPDC1	ENST00000456315.7	c.769+1353G>T		intron_variant	Intron 6 of 11	1	NM_001114120.3	ENSP00000412292.2
DEPDC1	ENST00000370966.9	c.769+1353G>T		intron_variant	Intron 6 of 10	1		ENSP00000360005.5
DEPDC1	ENST00000489862.1	n.472+1353G>T		intron_variant	Intron 6 of 12	1		ENSP00000436464.1

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85739 AN: 151688 Hom.: 25185 Cov.: 31

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.591

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.565 AC: 85764 AN: 151806 Hom.: 25183 Cov.: 31 AF XY: 0.552 AC XY: 40923 AN XY: 74190

African (AFR) AF: 0.593 AC: 24599 AN: 41448

American (AMR) AF: 0.485 AC: 7395 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.729 AC: 2527 AN: 3466

East Asian (EAS) AF: 0.182 AC: 936 AN: 5136

South Asian (SAS) AF: 0.415 AC: 1999 AN: 4814

European-Finnish (FIN) AF: 0.467 AC: 4921 AN: 10536

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41400 AN: 67864

Other (OTH) AF: 0.587 AC: 1238 AN: 2110

Alfa AF: 0.416 Hom.: 1095

Bravo AF: 0.568

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	11
DANN	Benign	0.68
PhyloP100		0.36
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4926344; hg19: chr1-68951267;