rs2037344

Positions:

• chr8-120007498-G-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.96).
• 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/exons	MANE	UniProt
DEPTOR	NM_022783.4	c.996+623G>A		intron_variant		ENST00000286234.6
DEPTOR	NM_001283012.2	c.693+623G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DEPTOR	ENST00000286234.6	c.996+623G>A		intron_variant		1	NM_022783.4	P1
DEPTOR	ENST00000523492.5	c.693+623G>A		intron_variant		2
DEPTOR	ENST00000518057.1	n.445+623G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.563

Gnomad4 AMR AF: 0.758

Gnomad4 ASJ AF: 0.739

Gnomad4 EAS AF: 0.710

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.741

Gnomad4 NFE AF: 0.723

Gnomad4 OTH AF: 0.704

Alfa AF: 0.723 Hom.: 74884

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

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: rs2037344; hg19: chr8-121019737;