chr10-122011788-C-A

Variant names:

• chr10-122011788-C-A
• rs12571870
• NM_206862.4:c.-45-10149C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_206862.4(TACC2):​c.-45-10149C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 152,010 control chromosomes in the GnomAD database, including 16,056 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 0.46 (16056 hom., cov: 32)
• Consequence: TACC2 NM_206862.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 6 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.598 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACC2	NM_206862.4	MANE Select	c.-45-10149C>A		intron	N/A	NP_996744.4
	TACC2	NM_001438364.1		c.-45-10149C>A		intron	N/A	NP_001425293.1
	TACC2	NM_001291877.2		c.-45-10149C>A		intron	N/A	NP_001278806.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACC2	ENST00000369005.6	TSL:1 MANE Select	c.-45-10149C>A		intron	N/A	ENSP00000358001.1
	TACC2	ENST00000515273.5	TSL:1	c.-45-10149C>A		intron	N/A	ENSP00000424467.1
	TACC2	ENST00000515603.5	TSL:1	c.-45-10149C>A		intron	N/A	ENSP00000427618.1

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69446 AN: 151892 Hom.: 16040 Cov.: 32

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.425

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.457 AC: 69508 AN: 152010 Hom.: 16056 Cov.: 32 AF XY: 0.461 AC XY: 34234 AN XY: 74284

African (AFR) AF: 0.507 AC: 21001 AN: 41454

American (AMR) AF: 0.421 AC: 6420 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1584 AN: 3468

East Asian (EAS) AF: 0.491 AC: 2544 AN: 5176

South Asian (SAS) AF: 0.617 AC: 2971 AN: 4818

European-Finnish (FIN) AF: 0.445 AC: 4699 AN: 10550

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.425 AC: 28909 AN: 67962

Other (OTH) AF: 0.436 AC: 921 AN: 2114

Alfa AF: 0.439 Hom.: 2516

Bravo AF: 0.449

Asia WGS AF: 0.552 AC: 1922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	10
DANN	Benign	0.87
PhyloP100		1.0
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: rs12571870; hg19: chr10-123771303;