8-119957445-C-G

Variant names:

• chr8-119957445-C-G
• rs9297608
• NM_022783.4:c.426-7787C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DEPTOR	NM_022783.4	c.426-7787C>G		intron_variant	Intron 3 of 8	ENST00000286234.6	NP_073620.2
DEPTOR	NM_001283012.2	c.123-7787C>G		intron_variant	Intron 1 of 6		NP_001269941.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DEPTOR	ENST00000286234.6	c.426-7787C>G		intron_variant	Intron 3 of 8	1	NM_022783.4	ENSP00000286234.5
DEPTOR	ENST00000523492.5	c.123-7787C>G		intron_variant	Intron 1 of 6	2		ENSP00000430457.1

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

African (AFR) AF: 0.547 AC: 22660 AN: 41412

American (AMR) AF: 0.734 AC: 11197 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.785 AC: 2723 AN: 3470

East Asian (EAS) AF: 0.610 AC: 3142 AN: 5154

South Asian (SAS) AF: 0.722 AC: 3477 AN: 4814

European-Finnish (FIN) AF: 0.768 AC: 8113 AN: 10560

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.715 AC: 48592 AN: 67970

Other (OTH) AF: 0.704 AC: 1479 AN: 2102

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
PhyloP100		-0.15
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: rs9297608; hg19: chr8-120969685;