chr1-68486881-AACACAC-A

Variant names:

• chr1-68486881-AACACAC-A
• rs55915411
• NM_001114120.3:c.769+50_769+55delGTGTGT

Variant summary

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

The NM_001114120.3(DEPDC1):​c.769+50_769+55delGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 1,167,950 control chromosomes in the GnomAD database, including 1,554 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.092 (628 hom., cov: 0)
  • Exomes 𝑓: 0.11 (926 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 (AMR) allele frequency at 95% confidence interval = 0.128 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+50_769+55delGTGTGT		intron	N/A	NP_001107592.1	Q5TB30-5
	DEPDC1	NM_017779.6		c.769+50_769+55delGTGTGT		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+50_769+55delGTGTGT		intron	N/A	ENSP00000412292.2	Q5TB30-5
	DEPDC1	ENST00000370966.9	TSL:1	c.769+50_769+55delGTGTGT		intron	N/A	ENSP00000360005.5	Q5TB30-2
	DEPDC1	ENST00000489862.1	TSL:1	n.472+50_472+55delGTGTGT		intron	N/A	ENSP00000436464.1	H0YES2

Frequencies

GnomAD3 genomes AF: 0.0917 AC: 13158 AN: 143566 Hom.: 626 Cov.: 0

Gnomad AFR AF: 0.0640

Gnomad AMI AF: 0.0168

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.0457

Gnomad EAS AF: 0.0851

Gnomad SAS AF: 0.0611

Gnomad FIN AF: 0.0960

Gnomad MID AF: 0.0752

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0830

GnomAD4 exome AF: 0.112 AC: 114581 AN: 1024292 Hom.: 926 AF XY: 0.111 AC XY: 55364 AN XY: 500884

African (AFR) AF: 0.0824 AC: 1842 AN: 22360

American (AMR) AF: 0.147 AC: 2632 AN: 17852

Ashkenazi Jewish (ASJ) AF: 0.0561 AC: 856 AN: 15268

East Asian (EAS) AF: 0.0630 AC: 1905 AN: 30218

South Asian (SAS) AF: 0.0661 AC: 1982 AN: 29984

European-Finnish (FIN) AF: 0.103 AC: 4255 AN: 41234

Middle Eastern (MID) AF: 0.0608 AC: 200 AN: 3292

European-Non Finnish (NFE) AF: 0.118 AC: 96804 AN: 822098

Other (OTH) AF: 0.0978 AC: 4105 AN: 41986

GnomAD4 genome AF: 0.0917 AC: 13175 AN: 143658 Hom.: 628 Cov.: 0 AF XY: 0.0918 AC XY: 6384 AN XY: 69574

African (AFR) AF: 0.0641 AC: 2494 AN: 38924

American (AMR) AF: 0.133 AC: 1879 AN: 14178

Ashkenazi Jewish (ASJ) AF: 0.0457 AC: 153 AN: 3346

East Asian (EAS) AF: 0.0847 AC: 410 AN: 4842

South Asian (SAS) AF: 0.0628 AC: 275 AN: 4378

European-Finnish (FIN) AF: 0.0960 AC: 905 AN: 9430

Middle Eastern (MID) AF: 0.0804 AC: 23 AN: 286

European-Non Finnish (NFE) AF: 0.105 AC: 6858 AN: 65404

Other (OTH) AF: 0.0824 AC: 163 AN: 1978

Alfa AF: 0.131 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

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

Other links and lift over

dbSNP: rs55915411; hg19: chr1-68952564;