rs10491168

chr17-63364102-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.2582+8712A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,174 control chromosomes in the GnomAD database, including 2,643 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 0.16 (2643 hom., cov: 32)
• Consequence: TANC2 NM_001394998.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170

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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TANC2	NM_001394998.1	c.2582+8712A>G		intron_variant		ENST00000689528.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TANC2	ENST00000689528.1	c.2582+8712A>G		intron_variant			NM_001394998.1	P3

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24922 AN: 152056 Hom.: 2643 Cov.: 32

Gnomad AFR AF: 0.0432

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.0708

Gnomad SAS AF: 0.0760

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.164 AC: 24918 AN: 152174 Hom.: 2643 Cov.: 32 AF XY: 0.160 AC XY: 11933 AN XY: 74396

Gnomad4 AFR AF: 0.0431

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.0706

Gnomad4 SAS AF: 0.0769

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.160

Alfa AF: 0.205 Hom.: 449

Bravo AF: 0.150

Asia WGS AF: 0.0830 AC: 289 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	9.6
Dann	Benign	0.83

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: rs10491168; hg19: chr17-61441463;