rs3763763

Variant names:

• chr10-122254089-C-A
• rs3763763
• NM_206862.4:c.*33C>A

Your query was ambiguous. Multiple possible variants found:

• chr10-122254089-C-A
• chr10-122254089-C-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_206862.4(TACC2):​c.*33C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 1,592,272 control chromosomes in the GnomAD database, including 51,511 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 0.26 (5021 hom., cov: 33)
  • Exomes 𝑓: 0.25 (46490 hom.)
• Consequence: TACC2 NM_206862.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.535
• Publications: 30 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.322 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACC2	NM_206862.4	MANE Select	c.*33C>A		3_prime_UTR	Exon 23 of 23	NP_996744.4	O95359-4
	TACC2	NM_001438364.1		c.*33C>A		3_prime_UTR	Exon 23 of 23	NP_001425293.1
	TACC2	NM_001291877.2		c.*33C>A		3_prime_UTR	Exon 20 of 20	NP_001278806.2	E9PBC6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACC2	ENST00000369005.6	TSL:1 MANE Select	c.*33C>A		3_prime_UTR	Exon 23 of 23	ENSP00000358001.1	O95359-4
	TACC2	ENST00000515273.5	TSL:1	c.*33C>A		3_prime_UTR	Exon 20 of 20	ENSP00000424467.1	E9PBC6
	TACC2	ENST00000515603.5	TSL:1	c.*33C>A		3_prime_UTR	Exon 20 of 20	ENSP00000427618.1	E7EMZ9

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38799 AN: 152080 Hom.: 5010 Cov.: 33

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.244

GnomAD2 exomes AF: 0.270 AC: 67861 AN: 251254 AF XY: 0.273

Gnomad AFR exome AF: 0.250

Gnomad AMR exome AF: 0.290

Gnomad ASJ exome AF: 0.273

Gnomad EAS exome AF: 0.261

Gnomad FIN exome AF: 0.290

Gnomad NFE exome AF: 0.245

Gnomad OTH exome AF: 0.271

GnomAD4 exome AF: 0.252 AC: 363047 AN: 1440074 Hom.: 46490 Cov.: 27 AF XY: 0.255 AC XY: 182793 AN XY: 717872

African (AFR) AF: 0.242 AC: 8001 AN: 33032

American (AMR) AF: 0.290 AC: 12952 AN: 44676

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 7042 AN: 26020

East Asian (EAS) AF: 0.270 AC: 10708 AN: 39590

South Asian (SAS) AF: 0.340 AC: 29140 AN: 85756

European-Finnish (FIN) AF: 0.291 AC: 15559 AN: 53388

Middle Eastern (MID) AF: 0.266 AC: 1527 AN: 5742

European-Non Finnish (NFE) AF: 0.241 AC: 262905 AN: 1092146

Other (OTH) AF: 0.255 AC: 15213 AN: 59724

GnomAD4 genome AF: 0.255 AC: 38856 AN: 152198 Hom.: 5021 Cov.: 33 AF XY: 0.261 AC XY: 19406 AN XY: 74420

African (AFR) AF: 0.246 AC: 10203 AN: 41512

American (AMR) AF: 0.278 AC: 4250 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 957 AN: 3468

East Asian (EAS) AF: 0.272 AC: 1410 AN: 5184

South Asian (SAS) AF: 0.336 AC: 1619 AN: 4824

European-Finnish (FIN) AF: 0.289 AC: 3061 AN: 10588

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16527 AN: 68018

Other (OTH) AF: 0.251 AC: 531 AN: 2114

Alfa AF: 0.246 Hom.: 15204

Bravo AF: 0.249

Asia WGS AF: 0.323 AC: 1125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	11
DANN	Benign	0.87
PhyloP100		0.54
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs3763763; hg19: chr10-124013604; COSMIC: COSV53278274; COSMIC: COSV53278274;