rs7386139

chr8-120015180-G-Achr8-120015180-G-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.92).
• 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/exons	MANE	UniProt
DEPTOR	NM_022783.4	c.1101+6047G>A		intron_variant		ENST00000286234.6
DEPTOR	NM_001283012.2	c.798+6047G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DEPTOR	ENST00000286234.6	c.1101+6047G>A		intron_variant		1	NM_022783.4	P1
DEPTOR	ENST00000523492.5	c.798+6047G>A		intron_variant		2
DEPTOR	ENST00000518057.1	n.550+6047G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.809

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.724

Gnomad4 FIN AF: 0.844

Gnomad4 NFE AF: 0.814

Gnomad4 OTH AF: 0.807

Alfa AF: 0.812 Hom.: 102209

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

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: rs7386139; hg19: chr8-121027419;