rs2037344

Variant names:

• chr8-120007498-G-A
• rs2037344
• NM_022783.4:c.996+623G>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.996+623G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 151,988 control chromosomes in the GnomAD database, including 35,826 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 0.68 (35826 hom., cov: 31)
• Consequence: DEPTOR NM_022783.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.44
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DEPTOR	NM_022783.4	c.996+623G>A		intron_variant	Intron 7 of 8	ENST00000286234.6	NP_073620.2
DEPTOR	NM_001283012.2	c.693+623G>A		intron_variant	Intron 5 of 6		NP_001269941.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DEPTOR	ENST00000286234.6	c.996+623G>A		intron_variant	Intron 7 of 8	1	NM_022783.4	ENSP00000286234.5
DEPTOR	ENST00000523492.5	c.693+623G>A		intron_variant	Intron 5 of 6	2		ENSP00000430457.1
DEPTOR	ENST00000518057.1	n.445+623G>A		intron_variant	Intron 4 of 5	5

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103554 AN: 151870 Hom.: 35825 Cov.: 31

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.768

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.709

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

GnomAD4 genome AF: 0.682 AC: 103605 AN: 151988 Hom.: 35826 Cov.: 31 AF XY: 0.684 AC XY: 50789 AN XY: 74286

African (AFR) AF: 0.563 AC: 23327 AN: 41412

American (AMR) AF: 0.758 AC: 11589 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.739 AC: 2565 AN: 3470

East Asian (EAS) AF: 0.710 AC: 3658 AN: 5154

South Asian (SAS) AF: 0.655 AC: 3148 AN: 4808

European-Finnish (FIN) AF: 0.741 AC: 7825 AN: 10566

Middle Eastern (MID) AF: 0.767 AC: 224 AN: 292

European-Non Finnish (NFE) AF: 0.723 AC: 49122 AN: 67982

Other (OTH) AF: 0.704 AC: 1484 AN: 2108

Alfa AF: 0.711 Hom.: 121462

Bravo AF: 0.684

Asia WGS AF: 0.645 AC: 2247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.031
DANN	Benign	0.73
PhyloP100		-2.4
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: rs2037344; hg19: chr8-121019737;