17-63316296-AAAGCTC-AAAGCTCAAGCTC

Variant names:

• chr17-63316296-A-AAAGCTC
• rs16715
• NM_001394998.1:c.1441+1634_1441+1639dupAAGCTC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001394998.1(TANC2):​c.1441+1634_1441+1639dupAAGCTC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.44 (18168 hom., cov: 0)
• Consequence: TANC2 NM_001394998.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TANC2	NM_001394998.1	c.1441+1634_1441+1639dupAAGCTC		intron_variant	Intron 10 of 27	ENST00000689528.1	NP_001381927.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TANC2	ENST00000689528.1	c.1441+1627_1441+1628insAAGCTC		intron_variant	Intron 10 of 27		NM_001394998.1	ENSP00000510600.1

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66567 AN: 151292 Hom.: 18119 Cov.: 0

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.0943

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.440 AC: 66673 AN: 151410 Hom.: 18168 Cov.: 0 AF XY: 0.438 AC XY: 32404 AN XY: 73992

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.0945

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.384

Alfa AF: 0.221 Hom.: 440

Asia WGS AF: 0.326 AC: 1137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs16715; hg19: chr17-61393657;