rs715827

Variant names:

• chr3-10270089-A-G
• rs715827
• NM_014760.4:c.949-42A>G

Variant summary

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

The NM_014760.4(TATDN2):​c.949-42A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 1,563,092 control chromosomes in the GnomAD database, including 40,813 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 0.20 (4448 hom., cov: 32)
  • Exomes 𝑓: 0.19 (36365 hom.)
• Consequence: TATDN2 NM_014760.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.673
• Publications: 13 publications found

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]

ENSG00000272410 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TATDN2	NM_014760.4	c.949-42A>G		intron_variant	Intron 3 of 7	ENST00000448281.7	NP_055575.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TATDN2	ENST00000448281.7	c.949-42A>G		intron_variant	Intron 3 of 7	1	NM_014760.4	ENSP00000408736.2
TATDN2	ENST00000287652.8	c.949-42A>G		intron_variant	Intron 3 of 7	1		ENSP00000287652.4
ENSG00000272410	ENST00000437082.5	n.778-42A>G		intron_variant	Intron 2 of 7	2		ENSP00000402783.1
ENSG00000272410	ENST00000450534.1	n.*393-42A>G		intron_variant	Intron 2 of 7	2		ENSP00000399689.1

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31144 AN: 152006 Hom.: 4445 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.189

GnomAD2 exomes AF: 0.289 AC: 60788 AN: 210360 AF XY: 0.281

Gnomad AFR exome AF: 0.172

Gnomad AMR exome AF: 0.549

Gnomad ASJ exome AF: 0.122

Gnomad EAS exome AF: 0.698

Gnomad FIN exome AF: 0.218

Gnomad NFE exome AF: 0.149

Gnomad OTH exome AF: 0.232

GnomAD4 exome AF: 0.189 AC: 266258 AN: 1410968 Hom.: 36365 Cov.: 32 AF XY: 0.193 AC XY: 134509 AN XY: 696448

African (AFR) AF: 0.167 AC: 5353 AN: 32116

American (AMR) AF: 0.525 AC: 20544 AN: 39156

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 2578 AN: 22304

East Asian (EAS) AF: 0.679 AC: 26740 AN: 39360

South Asian (SAS) AF: 0.415 AC: 31866 AN: 76824

European-Finnish (FIN) AF: 0.220 AC: 11225 AN: 50968

Middle Eastern (MID) AF: 0.179 AC: 763 AN: 4272

European-Non Finnish (NFE) AF: 0.143 AC: 155583 AN: 1087832

Other (OTH) AF: 0.200 AC: 11606 AN: 58136

GnomAD4 genome AF: 0.205 AC: 31151 AN: 152124 Hom.: 4448 Cov.: 32 AF XY: 0.217 AC XY: 16137 AN XY: 74376

African (AFR) AF: 0.171 AC: 7101 AN: 41516

American (AMR) AF: 0.355 AC: 5421 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 431 AN: 3470

East Asian (EAS) AF: 0.679 AC: 3506 AN: 5160

South Asian (SAS) AF: 0.443 AC: 2135 AN: 4820

European-Finnish (FIN) AF: 0.210 AC: 2219 AN: 10572

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9782 AN: 67986

Other (OTH) AF: 0.191 AC: 404 AN: 2116

Alfa AF: 0.178 Hom.: 8068

Bravo AF: 0.217

Asia WGS AF: 0.509 AC: 1766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.021
DANN	Benign	0.51
PhyloP100		-0.67
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: rs715827; hg19: chr3-10311773; COSMIC: COSV55054718; COSMIC: COSV55054718;