7-76483385-T-C

Position:

• chr7-76483385-T-C

Variant summary

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

The NM_001102594.3(DTX2):​c.908+238T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 136,610 control chromosomes in the GnomAD database, including 22,613 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 0.61 (22613 hom., cov: 33)
• Consequence: DTX2 NM_001102594.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

Genes affected

DTX2 (HGNC:15973): (deltex E3 ubiquitin ligase 2) DTX2 functions as an E3 ubiquitin ligase (Takeyama et al., 2003 [PubMed 12670957]).[supplied by OMIM, Nov 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DTX2	NM_001102594.3	c.908+238T>C		intron_variant		ENST00000430490.7	NP_001096064.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DTX2	ENST00000430490.7	c.908+238T>C		intron_variant		1	NM_001102594.3	ENSP00000411986.2

Frequencies

GnomAD3 genomes AF: 0.605 AC: 82647 AN: 136494 Hom.: 22570 Cov.: 33

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.616

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.606 AC: 82747 AN: 136610 Hom.: 22613 Cov.: 33 AF XY: 0.604 AC XY: 40226 AN XY: 66594

Gnomad4 AFR AF: 0.682

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.623

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.620

Alfa AF: 0.355 Hom.: 510

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.42
DANN	Benign	0.43

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: rs1799171; hg19: chr7-76112702;