rs17760362

chr17-63341306-T-A

Variant summary

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

The NM_001394998.1(TANC2):c.1807+974T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,240 control chromosomes in the GnomAD database, including 2,689 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 0.17 (2689 hom., cov: 32)
• Consequence: TANC2 NM_001394998.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.69

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=-0.73).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TANC2	NM_001394998.1	c.1807+974T>A		intron_variant		ENST00000689528.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TANC2	ENST00000689528.1	c.1807+974T>A		intron_variant			NM_001394998.1	P3
TANC2	ENST00000424789.6	c.1585+974T>A		intron_variant		1		A1
TANC2	ENST00000583356.5	c.1371+974T>A		intron_variant		1
TANC2	ENST00000389520.8	c.1585+974T>A		intron_variant		5		A1

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25178 AN: 152122 Hom.: 2689 Cov.: 32

Gnomad AFR AF: 0.0430

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.0702

Gnomad SAS AF: 0.0774

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.165 AC: 25174 AN: 152240 Hom.: 2689 Cov.: 32 AF XY: 0.162 AC XY: 12054 AN XY: 74410

Gnomad4 AFR AF: 0.0429

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.0700

Gnomad4 SAS AF: 0.0783

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.162

Alfa AF: 0.206 Hom.: 457

Bravo AF: 0.151

Asia WGS AF: 0.0840 AC: 290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	8.8
Dann	Benign	0.80

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: rs17760362; hg19: chr17-61418667;