rs7005380

Positions:

• chr8-119941633-G-A
• chr8-119941633-G-C
• chr8-119941633-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_022783.4(DEPTOR):​c.425+11695G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 151,892 control chromosomes in the GnomAD database, including 9,091 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 0.34 (9091 hom., cov: 32)
• Consequence: DEPTOR NM_022783.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650

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=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DEPTOR	NM_022783.4	c.425+11695G>A		intron_variant		ENST00000286234.6	NP_073620.2
DEPTOR	NM_001283012.2	c.123-23599G>A		intron_variant			NP_001269941.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DEPTOR	ENST00000286234.6	c.425+11695G>A		intron_variant		1	NM_022783.4	ENSP00000286234	P1
DEPTOR	ENST00000523492.5	c.123-23599G>A		intron_variant		2		ENSP00000430457

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50896 AN: 151772 Hom.: 9086 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.0688

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.335 AC: 50933 AN: 151892 Hom.: 9091 Cov.: 32 AF XY: 0.340 AC XY: 25249 AN XY: 74226

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.0681

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.320

Alfa AF: 0.353 Hom.: 4548

Bravo AF: 0.317

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.2
DANN	Benign	0.80

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: rs7005380; hg19: chr8-120953873;