rs7210972

chr17-63155117-A-G

Variant summary

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

The NM_001394998.1(TANC2):c.433+3737A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.564 in 151,604 control chromosomes in the GnomAD database, including 25,493 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 0.56 (25493 hom., cov: 30)
  • Failed GnomAD Quality Control
• Consequence: TANC2 NM_001394998.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.525

Genes affected

TANC2 (HGNC:30212): (tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2) Predicted to be involved in dense core granule cytoskeletal transport; regulation of dendritic spine development; and regulation of dendritic spine morphogenesis. Predicted to act upstream of or within in utero embryonic development. Located in dendritic spine. [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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TANC2	NM_001394998.1	c.433+3737A>G		intron_variant		ENST00000689528.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TANC2	ENST00000689528.1	c.433+3737A>G		intron_variant			NM_001394998.1	P3

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85469 AN: 151486 Hom.: 25450 Cov.: 30

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.510

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.564 AC: 85571 AN: 151604 Hom.: 25493 Cov.: 30 AF XY: 0.561 AC XY: 41501 AN XY: 74034

Gnomad4 AFR AF: 0.745

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.513

Alfa AF: 0.525 Hom.: 10409

Bravo AF: 0.560

Asia WGS AF: 0.409 AC: 1421 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.8
Dann	Benign	0.67

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: rs7210972; hg19: chr17-61232478;