17-63210084-T-G

Position:

• chr17-63210084-T-G

Variant summary

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

The NM_001394998.1(TANC2):​c.769+9127T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.585 in 152,004 control chromosomes in the GnomAD database, including 27,987 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 0.58 (27987 hom., cov: 31)
• Consequence: TANC2 NM_001394998.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.597

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TANC2	NM_001394998.1	c.769+9127T>G		intron_variant		ENST00000689528.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TANC2	ENST00000689528.1	c.769+9127T>G		intron_variant			NM_001394998.1	P3
	ENST00000581421.1	n.352-16014A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.585 AC: 88780 AN: 151886 Hom.: 27943 Cov.: 31

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.585 AC: 88884 AN: 152004 Hom.: 27987 Cov.: 31 AF XY: 0.580 AC XY: 43079 AN XY: 74290

Gnomad4 AFR AF: 0.816

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.527

Alfa AF: 0.501 Hom.: 7911

Bravo AF: 0.583

Asia WGS AF: 0.413 AC: 1440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.2
DANN	Benign	0.64

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: rs1518774; hg19: chr17-61287445;