1-68486881-AACACACACACACACACACACACACACAC-AACACACACACACACAC

Variant names:

• chr1-68486881-AACACACACACAC-A
• rs55915411
• NM_001114120.3:c.769+44_769+55delGTGTGTGTGTGT

Variant summary

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

The NM_001114120.3(DEPDC1):​c.769+44_769+55delGTGTGTGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000168 in 1,177,288 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 0.00022 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00016 (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+44_769+55delGTGTGTGTGTGT		intron	N/A	NP_001107592.1	Q5TB30-5
	DEPDC1	NM_017779.6		c.769+44_769+55delGTGTGTGTGTGT		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+44_769+55delGTGTGTGTGTGT		intron	N/A	ENSP00000412292.2	Q5TB30-5
	DEPDC1	ENST00000370966.9	TSL:1	c.769+44_769+55delGTGTGTGTGTGT		intron	N/A	ENSP00000360005.5	Q5TB30-2
	DEPDC1	ENST00000489862.1	TSL:1	n.472+44_472+55delGTGTGTGTGTGT		intron	N/A	ENSP00000436464.1	H0YES2

Frequencies

GnomAD3 genomes AF: 0.000223 AC: 32 AN: 143642 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000412

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000212

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000206

Gnomad SAS AF: 0.000228

Gnomad FIN AF: 0.000106

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000122

Gnomad OTH AF: 0.00102

GnomAD4 exome AF: 0.000161 AC: 166 AN: 1033646 Hom.: 0 AF XY: 0.000162 AC XY: 82 AN XY: 505484

African (AFR) AF: 0.000974 AC: 22 AN: 22576

American (AMR) AF: 0.000279 AC: 5 AN: 17934

Ashkenazi Jewish (ASJ) AF: 0.000194 AC: 3 AN: 15442

East Asian (EAS) AF: 0.000793 AC: 24 AN: 30268

South Asian (SAS) AF: 0.000166 AC: 5 AN: 30198

European-Finnish (FIN) AF: 0.0000482 AC: 2 AN: 41466

Middle Eastern (MID) AF: 0.00211 AC: 7 AN: 3316

European-Non Finnish (NFE) AF: 0.000106 AC: 88 AN: 830110

Other (OTH) AF: 0.000236 AC: 10 AN: 42336

GnomAD4 genome AF: 0.000223 AC: 32 AN: 143642 Hom.: 0 Cov.: 0 AF XY: 0.000173 AC XY: 12 AN XY: 69498

African (AFR) AF: 0.000412 AC: 16 AN: 38842

American (AMR) AF: 0.000212 AC: 3 AN: 14172

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

East Asian (EAS) AF: 0.000206 AC: 1 AN: 4854

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

European-Finnish (FIN) AF: 0.000106 AC: 1 AN: 9446

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

European-Non Finnish (NFE) AF: 0.000122 AC: 8 AN: 65428

Other (OTH) AF: 0.00102 AC: 2 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;