chr8-124501081-C-G

Variant names:

• chr8-124501081-C-G
• rs3886003
• NM_032026.4:c.593+3190G>C

Variant summary

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

The NM_032026.4(TATDN1):​c.593+3190G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 152,032 control chromosomes in the GnomAD database, including 24,329 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 0.55 (24329 hom., cov: 31)
• Consequence: TATDN1 NM_032026.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• Publications: 5 publications found

Genes affected

TATDN1 (HGNC:24220): (TatD DNase domain containing 1) Predicted to enable 3'-5'-exodeoxyribonuclease activity. Predicted to be involved in DNA metabolic process and nucleic acid phosphodiester bond hydrolysis. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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 = 0.736 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TATDN1	NM_032026.4	c.593+3190G>C		intron_variant	Intron 9 of 11	ENST00000276692.11	NP_114415.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TATDN1	ENST00000276692.11	c.593+3190G>C		intron_variant	Intron 9 of 11	1	NM_032026.4	ENSP00000276692.6

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83697 AN: 151914 Hom.: 24283 Cov.: 31

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.551 AC: 83781 AN: 152032 Hom.: 24329 Cov.: 31 AF XY: 0.551 AC XY: 40906 AN XY: 74296

African (AFR) AF: 0.743 AC: 30783 AN: 41454

American (AMR) AF: 0.476 AC: 7271 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1602 AN: 3472

East Asian (EAS) AF: 0.455 AC: 2345 AN: 5154

South Asian (SAS) AF: 0.538 AC: 2592 AN: 4820

European-Finnish (FIN) AF: 0.525 AC: 5542 AN: 10560

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 32042 AN: 67978

Other (OTH) AF: 0.530 AC: 1117 AN: 2108

Alfa AF: 0.510 Hom.: 2490

Bravo AF: 0.558

Asia WGS AF: 0.520 AC: 1804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.9
DANN	Benign	0.46
PhyloP100		0.31
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: rs3886003; hg19: chr8-125513322;