1-68486881-AACACACACACACACACACACACACACAC-AACACACACACACAC

Variant names:

• chr1-68486881-AACACACACACACAC-A
• rs55915411
• NM_001114120.3:c.769+42_769+55delGTGTGTGTGTGTGT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001114120.3(DEPDC1):​c.769+42_769+55delGTGTGTGTGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000713 in 1,177,440 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000097 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000068 (0 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: Uncertain_significance. The variant received 0 ACMG points.

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+42_769+55delGTGTGTGTGTGTGT		intron	N/A	NP_001107592.1	Q5TB30-5
	DEPDC1	NM_017779.6		c.769+42_769+55delGTGTGTGTGTGTGT		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+42_769+55delGTGTGTGTGTGTGT		intron	N/A	ENSP00000412292.2	Q5TB30-5
	DEPDC1	ENST00000370966.9	TSL:1	c.769+42_769+55delGTGTGTGTGTGTGT		intron	N/A	ENSP00000360005.5	Q5TB30-2
	DEPDC1	ENST00000489862.1	TSL:1	n.472+42_472+55delGTGTGTGTGTGTGT		intron	N/A	ENSP00000436464.1	H0YES2

Frequencies

GnomAD3 genomes AF: 0.0000975 AC: 14 AN: 143642 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000515

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000618

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000138

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000677 AC: 70 AN: 1033706 Hom.: 0 AF XY: 0.0000653 AC XY: 33 AN XY: 505510

African (AFR) AF: 0.0000885 AC: 2 AN: 22596

American (AMR) AF: 0.0000558 AC: 1 AN: 17934

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15442

East Asian (EAS) AF: 0.0000661 AC: 2 AN: 30270

South Asian (SAS) AF: 0.0000993 AC: 3 AN: 30200

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 41464

Middle Eastern (MID) AF: 0.000905 AC: 3 AN: 3316

European-Non Finnish (NFE) AF: 0.0000699 AC: 58 AN: 830146

Other (OTH) AF: 0.0000236 AC: 1 AN: 42338

GnomAD4 genome AF: 0.0000974 AC: 14 AN: 143734 Hom.: 0 Cov.: 0 AF XY: 0.0000862 AC XY: 6 AN XY: 69604

African (AFR) AF: 0.0000514 AC: 2 AN: 38948

American (AMR) AF: 0.00 AC: 0 AN: 14190

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3350

East Asian (EAS) AF: 0.000620 AC: 3 AN: 4842

South Asian (SAS) AF: 0.00 AC: 0 AN: 4380

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9446

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 286

European-Non Finnish (NFE) AF: 0.000138 AC: 9 AN: 65420

Other (OTH) AF: 0.00 AC: 0 AN: 1980

Alfa AF: 0.00 Hom.: 278

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.9

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;