rs12773310

Positions:

• chr10-122202239-T-A

Variant summary

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

The NM_206862.4(TACC2):​c.5971+7063T>A variant causes a intron change. The variant allele was found at a frequency of 0.248 in 149,446 control chromosomes in the GnomAD database, including 5,409 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 0.25 (5409 hom., cov: 23)
• Consequence: TACC2 NM_206862.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

Genes affected

TACC2 (HGNC:11523): (transforming acidic coiled-coil containing protein 2) Transforming acidic coiled-coil proteins are a conserved family of centrosome- and microtubule-interacting proteins that are implicated in cancer. This gene encodes a protein that concentrates at centrosomes throughout the cell cycle. This gene lies within a chromosomal region associated with tumorigenesis. Expression of this gene is induced by erythropoietin and is thought to affect the progression of breast tumors. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TACC2	NM_206862.4	c.5971+7063T>A		intron_variant		ENST00000369005.6	NP_996744.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TACC2	ENST00000369005.6	c.5971+7063T>A		intron_variant		1	NM_206862.4	ENSP00000358001

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37047 AN: 149328 Hom.: 5408 Cov.: 23

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.0365

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.248 AC: 37046 AN: 149446 Hom.: 5409 Cov.: 23 AF XY: 0.246 AC XY: 17928 AN XY: 72768

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.0364

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.330

Gnomad4 OTH AF: 0.257

Alfa AF: 0.293 Hom.: 790

Bravo AF: 0.228

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.2
DANN	Benign	0.29

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: rs12773310; hg19: chr10-123961754;