8-120035559-T-G

Variant names:

• chr8-120035559-T-G
• rs2326434
• NM_022783.4:c.1102-14017T>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.1102-14017T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 152,082 control chromosomes in the GnomAD database, including 53,341 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 0.83 (53341 hom., cov: 30)
• Consequence: DEPTOR NM_022783.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 5 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022783.4. 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
	DEPTOR	NM_022783.4	MANE Select	c.1102-14017T>G		intron	N/A	NP_073620.2	Q8TB45-1
	DEPTOR	NM_001283012.2		c.799-14017T>G		intron	N/A	NP_001269941.1	Q8TB45-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DEPTOR	ENST00000286234.6	TSL:1 MANE Select	c.1102-14017T>G		intron	N/A	ENSP00000286234.5	Q8TB45-1
	DEPTOR	ENST00000896812.1		c.1123-14017T>G		intron	N/A	ENSP00000566871.1
	DEPTOR	ENST00000896813.1		c.1120-14017T>G		intron	N/A	ENSP00000566872.1

Frequencies

GnomAD3 genomes AF: 0.835 AC: 126822 AN: 151964 Hom.: 53294 Cov.: 30

Gnomad AFR AF: 0.941

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.815

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.835 AC: 126922 AN: 152082 Hom.: 53341 Cov.: 30 AF XY: 0.834 AC XY: 62001 AN XY: 74334

African (AFR) AF: 0.941 AC: 39048 AN: 41508

American (AMR) AF: 0.815 AC: 12456 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.809 AC: 2808 AN: 3470

East Asian (EAS) AF: 0.719 AC: 3688 AN: 5128

South Asian (SAS) AF: 0.747 AC: 3591 AN: 4806

European-Finnish (FIN) AF: 0.819 AC: 8675 AN: 10586

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.793 AC: 53910 AN: 67986

Other (OTH) AF: 0.820 AC: 1731 AN: 2110

Alfa AF: 0.804 Hom.: 27142

Bravo AF: 0.841

Asia WGS AF: 0.701 AC: 2440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.15
DANN	Benign	0.64
PhyloP100		-1.7
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: rs2326434; hg19: chr8-121047798;