rs1010657

Variant names:

• chr10-122238202-A-G
• rs1010657
• NM_206862.4:c.8348+165A>G

Variant summary

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

The NM_206862.4(TACC2):​c.8348+165A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 152,056 control chromosomes in the GnomAD database, including 10,879 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 0.36 (10879 hom., cov: 32)
• Consequence: TACC2 NM_206862.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16

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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TACC2	NM_206862.4	c.8348+165A>G		intron_variant	Intron 18 of 22	ENST00000369005.6	NP_996744.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TACC2	ENST00000369005.6	c.8348+165A>G		intron_variant	Intron 18 of 22	1	NM_206862.4	ENSP00000358001.1

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54569 AN: 151938 Hom.: 10862 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.359 AC: 54606 AN: 152056 Hom.: 10879 Cov.: 32 AF XY: 0.362 AC XY: 26893 AN XY: 74332

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.419

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.414

Alfa AF: 0.423 Hom.: 17994

Bravo AF: 0.348

Asia WGS AF: 0.468 AC: 1630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0080
DANN	Benign	0.44

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: rs1010657; hg19: chr10-123997717; COSMIC: COSV53281386; COSMIC: COSV53281386;