3-10280050-C-T

Position:

• chr3-10280050-C-T

Variant summary

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

The ENST00000448281.7(TATDN2):​c.*868C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 153,742 control chromosomes in the GnomAD database, including 5,687 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 0.26 (5669 hom., cov: 32)
  • Exomes 𝑓: 0.18 (18 hom.)
• Consequence: TATDN2 ENST00000448281.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

Genes affected

TATDN2 (HGNC:28988): (TatD DNase domain containing 2) Predicted to enable metal ion binding activity and nuclease activity. Predicted to be involved in nucleic acid phosphodiester bond hydrolysis. Predicted to be located in nucleoplasm. [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=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TATDN2	NM_014760.4	c.*868C>T		3_prime_UTR_variant	8/8	ENST00000448281.7	NP_055575.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TATDN2	ENST00000448281.7	c.*868C>T		3_prime_UTR_variant	8/8	1	NM_014760.4	ENSP00000408736	P1
TATDN2	ENST00000287652.8	c.*839C>T		3_prime_UTR_variant	8/8	1		ENSP00000287652	P1
TATDN2	ENST00000496355.1	n.1373C>T		non_coding_transcript_exon_variant	5/5	3

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39777 AN: 152020 Hom.: 5651 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.412

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.0239

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.271

GnomAD4 exome AF: 0.179 AC: 287 AN: 1604 Hom.: 18 Cov.: 0 AF XY: 0.174 AC XY: 147 AN XY: 844

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.181

Gnomad4 NFE exome AF: 0.125

Gnomad4 OTH exome AF: 0.188

GnomAD4 genome AF: 0.262 AC: 39840 AN: 152138 Hom.: 5669 Cov.: 32 AF XY: 0.257 AC XY: 19142 AN XY: 74368

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.0237

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.268

Alfa AF: 0.241 Hom.: 7666

Bravo AF: 0.264

Asia WGS AF: 0.135 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.3
DANN	Benign	0.85
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

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: rs514658; hg19: chr3-10321734; COSMIC: COSV55054727; COSMIC: COSV55054727;