rs2326434

Variant names:

• chr8-120035559-T-A
• rs2326434
• NM_022783.4:c.1102-14017T>A

Your query was ambiguous. Multiple possible variants found:

• chr8-120035559-T-A
• chr8-120035559-T-C
• chr8-120035559-T-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_022783.4(DEPTOR):​c.1102-14017T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
• Consequence: DEPTOR NM_022783.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DEPTOR	NM_022783.4	c.1102-14017T>A		intron_variant	Intron 8 of 8	ENST00000286234.6	NP_073620.2
DEPTOR	NM_001283012.2	c.799-14017T>A		intron_variant	Intron 6 of 6		NP_001269941.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DEPTOR	ENST00000286234.6	c.1102-14017T>A		intron_variant	Intron 8 of 8	1	NM_022783.4	ENSP00000286234.5
DEPTOR	ENST00000523492.5	c.799-14017T>A		intron_variant	Intron 6 of 6	2		ENSP00000430457.1
DEPTOR	ENST00000518057.1	n.551-14017T>A		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.19
DANN	Benign	0.35

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: rs2326434; hg19: chr8-121047798;