rs10887058

chr10-122054244-A-G

Variant summary

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

The NM_206862.4(TACC2):c.146+3694A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,190 control chromosomes in the GnomAD database, including 5,729 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 (5729 hom., cov: 33)
• Consequence: TACC2 NM_206862.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TACC2	NM_206862.4	c.146+3694A>G		intron_variant		ENST00000369005.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TACC2	ENST00000369005.6	c.146+3694A>G		intron_variant		1	NM_206862.4

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37806 AN: 152072 Hom.: 5724 Cov.: 33

Gnomad AFR AF: 0.0837

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.248 AC: 37817 AN: 152190 Hom.: 5729 Cov.: 33 AF XY: 0.247 AC XY: 18345 AN XY: 74390

Gnomad4 AFR AF: 0.0835

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.249

Alfa AF: 0.319 Hom.: 5835

Bravo AF: 0.233

Asia WGS AF: 0.246 AC: 857 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	0.23
Dann	Benign	0.74

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: rs10887058; hg19: chr10-123813759;