rs2447442

Positions:

• chr17-63240716-C-T

Variant summary

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

The NM_001394998.1(TANC2):​c.1033+2639C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 152,014 control chromosomes in the GnomAD database, including 28,986 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 0.59 (28986 hom., cov: 32)
• Consequence: TANC2 NM_001394998.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.887

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]

ENSG00000233635 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TANC2	NM_001394998.1	c.1033+2639C>T		intron_variant		ENST00000689528.1	NP_001381927.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TANC2	ENST00000689528.1	c.1033+2639C>T		intron_variant			NM_001394998.1	ENSP00000510600.1

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89985 AN: 151896 Hom.: 28932 Cov.: 32

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.593 AC: 90096 AN: 152014 Hom.: 28986 Cov.: 32 AF XY: 0.588 AC XY: 43650 AN XY: 74272

Gnomad4 AFR AF: 0.844

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.535

Alfa AF: 0.532 Hom.: 10103

Bravo AF: 0.593

Asia WGS AF: 0.410 AC: 1428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.70
DANN	Benign	0.34

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: rs2447442; hg19: chr17-61318077; COSMIC: COSV67340691;