rs3750839

Positions:

• chr10-122013392-G-A
• chr10-122013392-G-C

Variant summary

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

The NM_206862.4(TACC2):​c.-45-8545G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,142 control chromosomes in the GnomAD database, including 2,051 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 0.16 (2051 hom., cov: 32)
• Consequence: TACC2 NM_206862.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228

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=-0.59).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TACC2	NM_206862.4	c.-45-8545G>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.-45-8545G>A		intron_variant		1	NM_206862.4	ENSP00000358001.1

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24110 AN: 152024 Hom.: 2054 Cov.: 32

Gnomad AFR AF: 0.0998

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.158 AC: 24106 AN: 152142 Hom.: 2051 Cov.: 32 AF XY: 0.156 AC XY: 11630 AN XY: 74384

Gnomad4 AFR AF: 0.0997

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.176

Alfa AF: 0.176 Hom.: 2801

Bravo AF: 0.151

Asia WGS AF: 0.115 AC: 401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	13
DANN	Benign	0.83

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3750839; hg19: chr10-123772907;