rs9297608

chr8-119957445-C-Gchr8-119957445-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022783.4(DEPTOR):c.426-7787C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 151,938 control chromosomes in the GnomAD database, including 34,870 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.67 (34870 hom., cov: 31)
• Consequence: DEPTOR NM_022783.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155

Genes affected

DEPTOR (HGNC:22953): (DEP domain containing MTOR interacting protein) Involved in several processes, including negative regulation of TOR signaling; negative regulation of cell size; and negative regulation of protein kinase activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DEPTOR	NM_022783.4	c.426-7787C>G		intron_variant		ENST00000286234.6
DEPTOR	NM_001283012.2	c.123-7787C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DEPTOR	ENST00000286234.6	c.426-7787C>G		intron_variant		1	NM_022783.4	P1
DEPTOR	ENST00000523492.5	c.123-7787C>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102267 AN: 151820 Hom.: 34868 Cov.: 31

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.722

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.709

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.673 AC: 102307 AN: 151938 Hom.: 34870 Cov.: 31 AF XY: 0.678 AC XY: 50349 AN XY: 74246

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.734

Gnomad4 ASJ AF: 0.785

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.722

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.704

Alfa AF: 0.689 Hom.: 4291

Bravo AF: 0.670

Asia WGS AF: 0.636 AC: 2214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.78
Dann	Benign	0.43

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

Publications

LitVar

Other links and lift over

dbSNP: rs9297608; hg19: chr8-120969685;