1-68486881-AACAC-A

Variant names:

• chr1-68486881-AACAC-A
• rs55915411
• NM_001114120.3:c.769+52_769+55delGTGT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001114120.3(DEPDC1):​c.769+52_769+55delGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 1,145,606 control chromosomes in the GnomAD database, including 2,011 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.12 (1115 hom., cov: 0)
  • Exomes 𝑓: 0.17 (896 hom.)
• Consequence: DEPDC1 NM_001114120.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.95
• 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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001114120.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DEPDC1	NM_001114120.3	MANE Select	c.769+52_769+55delGTGT		intron	N/A	NP_001107592.1	Q5TB30-5
	DEPDC1	NM_017779.6		c.769+52_769+55delGTGT		intron	N/A	NP_060249.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DEPDC1	ENST00000456315.7	TSL:1 MANE Select	c.769+52_769+55delGTGT		intron	N/A	ENSP00000412292.2	Q5TB30-5
	DEPDC1	ENST00000370966.9	TSL:1	c.769+52_769+55delGTGT		intron	N/A	ENSP00000360005.5	Q5TB30-2
	DEPDC1	ENST00000489862.1	TSL:1	n.472+52_472+55delGTGT		intron	N/A	ENSP00000436464.1	H0YES2

Frequencies

GnomAD3 genomes AF: 0.122 AC: 17538 AN: 143434 Hom.: 1111 Cov.: 0

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.0874

Gnomad AMR AF: 0.0833

Gnomad ASJ AF: 0.0998

Gnomad EAS AF: 0.0225

Gnomad SAS AF: 0.0639

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.115

GnomAD4 exome AF: 0.174 AC: 174224 AN: 1002082 Hom.: 896 AF XY: 0.173 AC XY: 84834 AN XY: 489580

African (AFR) AF: 0.204 AC: 4538 AN: 22242

American (AMR) AF: 0.0979 AC: 1715 AN: 17520

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 3232 AN: 14446

East Asian (EAS) AF: 0.0263 AC: 784 AN: 29760

South Asian (SAS) AF: 0.115 AC: 3413 AN: 29624

European-Finnish (FIN) AF: 0.147 AC: 5826 AN: 39748

Middle Eastern (MID) AF: 0.171 AC: 539 AN: 3148

European-Non Finnish (NFE) AF: 0.183 AC: 147199 AN: 804726

Other (OTH) AF: 0.171 AC: 6978 AN: 40868

GnomAD4 genome AF: 0.122 AC: 17561 AN: 143524 Hom.: 1115 Cov.: 0 AF XY: 0.120 AC XY: 8361 AN XY: 69472

African (AFR) AF: 0.189 AC: 7363 AN: 38910

American (AMR) AF: 0.0831 AC: 1179 AN: 14180

Ashkenazi Jewish (ASJ) AF: 0.0998 AC: 334 AN: 3346

East Asian (EAS) AF: 0.0227 AC: 110 AN: 4840

South Asian (SAS) AF: 0.0651 AC: 285 AN: 4376

European-Finnish (FIN) AF: 0.109 AC: 1019 AN: 9382

Middle Eastern (MID) AF: 0.106 AC: 30 AN: 284

European-Non Finnish (NFE) AF: 0.106 AC: 6936 AN: 65334

Other (OTH) AF: 0.115 AC: 227 AN: 1980

Alfa AF: 0.0552 Hom.: 278

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.9
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: rs55915411; hg19: chr1-68952564; COSMIC: COSV63957739; COSMIC: COSV63957739;