10-122092312-C-T

Variant names:

• chr10-122092312-C-T
• rs11200392
• NM_206862.4:c.5573+3721C>T

Variant summary

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

The NM_206862.4(TACC2):​c.5573+3721C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,084 control chromosomes in the GnomAD database, including 6,460 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 0.29 (6460 hom., cov: 33)
• Consequence: TACC2 NM_206862.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 9 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TACC2	NM_206862.4	c.5573+3721C>T		intron_variant	Intron 5 of 22	ENST00000369005.6	NP_996744.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TACC2	ENST00000369005.6	c.5573+3721C>T		intron_variant	Intron 5 of 22	1	NM_206862.4	ENSP00000358001.1

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43307 AN: 151966 Hom.: 6440 Cov.: 33

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.285 AC: 43382 AN: 152084 Hom.: 6460 Cov.: 33 AF XY: 0.288 AC XY: 21450 AN XY: 74356

African (AFR) AF: 0.331 AC: 13728 AN: 41488

American (AMR) AF: 0.311 AC: 4749 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 880 AN: 3466

East Asian (EAS) AF: 0.379 AC: 1958 AN: 5170

South Asian (SAS) AF: 0.422 AC: 2031 AN: 4816

European-Finnish (FIN) AF: 0.274 AC: 2896 AN: 10580

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16173 AN: 67982

Other (OTH) AF: 0.287 AC: 606 AN: 2110

Alfa AF: 0.260 Hom.: 10617

Bravo AF: 0.289

Asia WGS AF: 0.400 AC: 1387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.7
DANN	Benign	0.34
PhyloP100		0.078
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: rs11200392; hg19: chr10-123851827;