1-68486881-AACACACACACACACACACACACACACAC-AACACACACACAC

Variant names:

• chr1-68486881-AACACACACACACACAC-A
• rs55915411
• NM_001114120.3:c.769+40_769+55delGTGTGTGTGTGTGTGT

Variant summary

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

The NM_001114120.3(DEPDC1):​c.769+40_769+55delGTGTGTGTGTGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000442 in 1,177,356 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 0.00010 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000036 (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+40_769+55delGTGTGTGTGTGTGTGT		intron	N/A	NP_001107592.1	Q5TB30-5
	DEPDC1	NM_017779.6		c.769+40_769+55delGTGTGTGTGTGTGTGT		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+40_769+55delGTGTGTGTGTGTGTGT		intron	N/A	ENSP00000412292.2	Q5TB30-5
	DEPDC1	ENST00000370966.9	TSL:1	c.769+40_769+55delGTGTGTGTGTGTGTGT		intron	N/A	ENSP00000360005.5	Q5TB30-2
	DEPDC1	ENST00000489862.1	TSL:1	n.472+40_472+55delGTGTGTGTGTGTGTGT		intron	N/A	ENSP00000436464.1	H0YES2

Frequencies

GnomAD3 genomes AF: 0.000104 AC: 15 AN: 143644 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000257

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000228

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000611

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000358 AC: 37 AN: 1033712 Hom.: 0 AF XY: 0.0000455 AC XY: 23 AN XY: 505512

African (AFR) AF: 0.000266 AC: 6 AN: 22598

American (AMR) AF: 0.00 AC: 0 AN: 17934

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

East Asian (EAS) AF: 0.0000330 AC: 1 AN: 30270

South Asian (SAS) AF: 0.000232 AC: 7 AN: 30200

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 41466

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3316

European-Non Finnish (NFE) AF: 0.0000241 AC: 20 AN: 830148

Other (OTH) AF: 0.0000709 AC: 3 AN: 42338

GnomAD4 genome AF: 0.000104 AC: 15 AN: 143644 Hom.: 0 Cov.: 0 AF XY: 0.0000432 AC XY: 3 AN XY: 69500

African (AFR) AF: 0.000257 AC: 10 AN: 38842

American (AMR) AF: 0.00 AC: 0 AN: 14172

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

East Asian (EAS) AF: 0.00 AC: 0 AN: 4854

South Asian (SAS) AF: 0.000228 AC: 1 AN: 4386

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

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 306

European-Non Finnish (NFE) AF: 0.0000611 AC: 4 AN: 65430

Other (OTH) AF: 0.00 AC: 0 AN: 1966

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;