NM_022783.4:c.1101+6047G>A

Variant names:

• chr8-120015180-G-A
• rs7386139
• NM_022783.4:c.1101+6047G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022783.4(DEPTOR):​c.1101+6047G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.81 in 152,120 control chromosomes in the GnomAD database, including 49,923 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 0.81 (49923 hom., cov: 31)
• Consequence: DEPTOR NM_022783.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 10 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DEPTOR	NM_022783.4	c.1101+6047G>A		intron_variant	Intron 8 of 8	ENST00000286234.6	NP_073620.2
DEPTOR	NM_001283012.2	c.798+6047G>A		intron_variant	Intron 6 of 6		NP_001269941.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DEPTOR	ENST00000286234.6	c.1101+6047G>A		intron_variant	Intron 8 of 8	1	NM_022783.4	ENSP00000286234.5
DEPTOR	ENST00000523492.5	c.798+6047G>A		intron_variant	Intron 6 of 6	2		ENSP00000430457.1
DEPTOR	ENST00000518057.1	n.550+6047G>A		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes AF: 0.810 AC: 123097 AN: 152002 Hom.: 49906 Cov.: 31

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.810 AC: 123164 AN: 152120 Hom.: 49923 Cov.: 31 AF XY: 0.809 AC XY: 60153 AN XY: 74372

African (AFR) AF: 0.817 AC: 33859 AN: 41460

American (AMR) AF: 0.811 AC: 12402 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.809 AC: 2806 AN: 3470

East Asian (EAS) AF: 0.712 AC: 3681 AN: 5172

South Asian (SAS) AF: 0.724 AC: 3489 AN: 4818

European-Finnish (FIN) AF: 0.844 AC: 8946 AN: 10600

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.814 AC: 55335 AN: 67994

Other (OTH) AF: 0.807 AC: 1701 AN: 2108

Alfa AF: 0.812 Hom.: 215540

Bravo AF: 0.812

Asia WGS AF: 0.683 AC: 2377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.37
PhyloP100		-1.1
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: rs7386139; hg19: chr8-121027419;