7-76483385-T-C

Variant names:

• chr7-76483385-T-C
• rs1799171
• NM_001102594.3:c.908+238T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001102594.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DTX2	NM_001102594.3	MANE Select	c.908+238T>C		intron	N/A	NP_001096064.1
	DTX2	NM_001102595.3		c.908+238T>C		intron	N/A	NP_001096065.1
	DTX2	NM_020892.4		c.908+238T>C		intron	N/A	NP_065943.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DTX2	ENST00000430490.7	TSL:1 MANE Select	c.908+238T>C		intron	N/A	ENSP00000411986.2
	DTX2	ENST00000324432.9	TSL:1	c.908+238T>C		intron	N/A	ENSP00000322885.5
	DTX2	ENST00000413936.6	TSL:1	c.908+238T>C		intron	N/A	ENSP00000390218.2

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

African (AFR) AF: 0.682 AC: 26180 AN: 38406

American (AMR) AF: 0.591 AC: 8243 AN: 13936

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2119 AN: 3282

East Asian (EAS) AF: 0.623 AC: 2966 AN: 4764

South Asian (SAS) AF: 0.665 AC: 3015 AN: 4532

European-Finnish (FIN) AF: 0.473 AC: 4057 AN: 8574

Middle Eastern (MID) AF: 0.620 AC: 165 AN: 266

European-Non Finnish (NFE) AF: 0.572 AC: 34393 AN: 60178

Other (OTH) AF: 0.620 AC: 1187 AN: 1916

Alfa AF: 0.355 Hom.: 510

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.42
DANN	Benign	0.43
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1799171; hg19: chr7-76112702;