rs17103129

Positions:

• chr10-122150884-T-C

Variant summary

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

The NM_206862.4(TACC2):​c.5834+7178T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0392 in 152,268 control chromosomes in the GnomAD database, including 216 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 0.039 (216 hom., cov: 32)
• Consequence: TACC2 NM_206862.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.353

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]

TACC2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TACC2	NM_206862.4	c.5834+7178T>C		intron_variant		ENST00000369005.6	NP_996744.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TACC2	ENST00000369005.6	c.5834+7178T>C		intron_variant		1	NM_206862.4	ENSP00000358001.1

Frequencies

GnomAD3 genomes AF: 0.0392 AC: 5970 AN: 152150 Hom.: 216 Cov.: 32

Gnomad AFR AF: 0.00915

Gnomad AMI AF: 0.0473

Gnomad AMR AF: 0.0522

Gnomad ASJ AF: 0.0415

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.0477

Gnomad FIN AF: 0.0412

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0436

Gnomad OTH AF: 0.0420

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

GnomAD4 genome AF: 0.0392 AC: 5970 AN: 152268 Hom.: 216 Cov.: 32 AF XY: 0.0404 AC XY: 3006 AN XY: 74434

Gnomad4 AFR AF: 0.00912

Gnomad4 AMR AF: 0.0522

Gnomad4 ASJ AF: 0.0415

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.0477

Gnomad4 FIN AF: 0.0412

Gnomad4 NFE AF: 0.0436

Gnomad4 OTH AF: 0.0421

Alfa AF: 0.0396 Hom.: 44

Bravo AF: 0.0391

Asia WGS AF: 0.0850 AC: 294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.2
DANN	Benign	0.72

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: rs17103129; hg19: chr10-123910399;