rs7840156

Variant names:

• chr8-119873704-T-C
• rs7840156
• ENST00000500705.3:n.785A>G

Variant summary

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

The ENST00000500705.3(DEPTOR-AS1):​n.785A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 1,227,428 control chromosomes in the GnomAD database, including 63,792 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 (9506 hom., cov: 33)
  • Exomes 𝑓: 0.31 (54286 hom.)
• Consequence: DEPTOR-AS1 ENST00000500705.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.506
• Publications: 5 publications found

Genes affected

DEPTOR-AS1 (HGNC:55602): (DEPTOR antisense RNA 1)

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=-0.69).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DEPTOR	NM_022783.4	c.-143T>C		upstream_gene_variant		ENST00000286234.6	NP_073620.2
DEPTOR	NM_001283012.2	c.-143T>C		upstream_gene_variant			NP_001269941.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DEPTOR	ENST00000286234.6	c.-143T>C		upstream_gene_variant		1	NM_022783.4	ENSP00000286234.5

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51596 AN: 152018 Hom.: 9498 Cov.: 33

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.0541

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.292

GnomAD4 exome AF: 0.308 AC: 330957 AN: 1075290 Hom.: 54286 Cov.: 14 AF XY: 0.313 AC XY: 165424 AN XY: 528628

African (AFR) AF: 0.471 AC: 10312 AN: 21914

American (AMR) AF: 0.212 AC: 3616 AN: 17062

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 5423 AN: 17134

East Asian (EAS) AF: 0.0566 AC: 1683 AN: 29760

South Asian (SAS) AF: 0.507 AC: 28547 AN: 56264

European-Finnish (FIN) AF: 0.327 AC: 12581 AN: 38486

Middle Eastern (MID) AF: 0.297 AC: 956 AN: 3220

European-Non Finnish (NFE) AF: 0.300 AC: 253904 AN: 845306

Other (OTH) AF: 0.302 AC: 13935 AN: 46144

GnomAD4 genome AF: 0.339 AC: 51649 AN: 152138 Hom.: 9506 Cov.: 33 AF XY: 0.338 AC XY: 25173 AN XY: 74372

African (AFR) AF: 0.451 AC: 18718 AN: 41518

American (AMR) AF: 0.224 AC: 3424 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1127 AN: 3472

East Asian (EAS) AF: 0.0536 AC: 276 AN: 5148

South Asian (SAS) AF: 0.505 AC: 2434 AN: 4818

European-Finnish (FIN) AF: 0.343 AC: 3627 AN: 10586

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 21018 AN: 67984

Other (OTH) AF: 0.291 AC: 613 AN: 2108

Alfa AF: 0.340 Hom.: 1175

Bravo AF: 0.328

Asia WGS AF: 0.294 AC: 1023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	16
DANN	Benign	0.73
PhyloP100		0.51
PromoterAI		0.0080	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7840156; hg19: chr8-120885944; COSMIC: COSV53815587;