1-68486881-AACACACACACACACACACACACACACAC-AACACACACACACACACACACACACAC

Variant names:

• chr1-68486881-AAC-A
• rs55915411
• NM_001114120.3:c.769+54_769+55delGT

Variant summary

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

The NM_001114120.3(DEPDC1):​c.769+54_769+55delGT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.35 (9248 hom., cov: 0)
  • Exomes 𝑓: 0.34 (8486 hom.)
  • Failed GnomAD Quality Control
• Consequence: DEPDC1 NM_001114120.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54
• 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 (NFE) allele frequency at 95% confidence interval = 0.428 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+54_769+55delGT		intron	N/A	NP_001107592.1	Q5TB30-5
	DEPDC1	NM_017779.6		c.769+54_769+55delGT		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+54_769+55delGT		intron	N/A	ENSP00000412292.2	Q5TB30-5
	DEPDC1	ENST00000370966.9	TSL:1	c.769+54_769+55delGT		intron	N/A	ENSP00000360005.5	Q5TB30-2
	DEPDC1	ENST00000489862.1	TSL:1	n.472+54_472+55delGT		intron	N/A	ENSP00000436464.1	H0YES2

Frequencies

GnomAD3 genomes AF: 0.349 AC: 50019 AN: 143328 Hom.: 9252 Cov.: 0

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.0789

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.373

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.342 AC: 345042 AN: 1007684 Hom.: 8486 AF XY: 0.343 AC XY: 168924 AN XY: 492898

African (AFR) AF: 0.239 AC: 5237 AN: 21926

American (AMR) AF: 0.272 AC: 4694 AN: 17284

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 6262 AN: 15220

East Asian (EAS) AF: 0.289 AC: 7554 AN: 26180

South Asian (SAS) AF: 0.303 AC: 8947 AN: 29552

European-Finnish (FIN) AF: 0.327 AC: 13165 AN: 40316

Middle Eastern (MID) AF: 0.401 AC: 1319 AN: 3286

European-Non Finnish (NFE) AF: 0.349 AC: 283601 AN: 812648

Other (OTH) AF: 0.346 AC: 14263 AN: 41272

GnomAD4 genome AF: 0.349 AC: 50021 AN: 143420 Hom.: 9248 Cov.: 0 AF XY: 0.341 AC XY: 23679 AN XY: 69442

African (AFR) AF: 0.235 AC: 9142 AN: 38886

American (AMR) AF: 0.321 AC: 4543 AN: 14150

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1845 AN: 3344

East Asian (EAS) AF: 0.0789 AC: 382 AN: 4840

South Asian (SAS) AF: 0.298 AC: 1302 AN: 4372

European-Finnish (FIN) AF: 0.351 AC: 3296 AN: 9398

Middle Eastern (MID) AF: 0.524 AC: 150 AN: 286

European-Non Finnish (NFE) AF: 0.432 AC: 28234 AN: 65286

Other (OTH) AF: 0.371 AC: 730 AN: 1968

Alfa AF: 0.274 Hom.: 278

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.5
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;