rs12773310

Variant names:

• chr10-122202239-T-A
• rs12773310
• NM_206862.4:c.5971+7063T>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_206862.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACC2	NM_206862.4	MANE Select	c.5971+7063T>A		intron	N/A	NP_996744.4
	TACC2	NM_001438364.1		c.5896+7063T>A		intron	N/A	NP_001425293.1
	TACC2	NM_001291877.2		c.5983+7063T>A		intron	N/A	NP_001278806.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACC2	ENST00000369005.6	TSL:1 MANE Select	c.5971+7063T>A		intron	N/A	ENSP00000358001.1
	TACC2	ENST00000515273.5	TSL:1	c.5983+7063T>A		intron	N/A	ENSP00000424467.1
	TACC2	ENST00000515603.5	TSL:1	c.5836+7063T>A		intron	N/A	ENSP00000427618.1

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

African (AFR) AF: 0.118 AC: 4797 AN: 40792

American (AMR) AF: 0.215 AC: 3226 AN: 15008

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1167 AN: 3450

East Asian (EAS) AF: 0.0364 AC: 187 AN: 5132

South Asian (SAS) AF: 0.275 AC: 1260 AN: 4584

European-Finnish (FIN) AF: 0.331 AC: 3313 AN: 9998

Middle Eastern (MID) AF: 0.269 AC: 78 AN: 290

European-Non Finnish (NFE) AF: 0.330 AC: 22212 AN: 67228

Other (OTH) AF: 0.257 AC: 530 AN: 2062

Alfa AF: 0.293 Hom.: 790

Bravo AF: 0.228

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.2
DANN	Benign	0.29
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12773310; hg19: chr10-123961754;