10-122187328-C-T

Variant names:

• chr10-122187328-C-T
• rs7920046
• NM_206862.4:c.5835-7712C>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.5835-7712C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 151,920 control chromosomes in the GnomAD database, including 21,364 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 0.52 (21364 hom., cov: 31)
• Consequence: TACC2 NM_206862.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387
• Publications: 2 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TACC2	NM_206862.4	c.5835-7712C>T		intron_variant	Intron 7 of 22	ENST00000369005.6	NP_996744.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TACC2	ENST00000369005.6	c.5835-7712C>T		intron_variant	Intron 7 of 22	1	NM_206862.4	ENSP00000358001.1

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79201 AN: 151802 Hom.: 21341 Cov.: 31

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.522 AC: 79261 AN: 151920 Hom.: 21364 Cov.: 31 AF XY: 0.528 AC XY: 39167 AN XY: 74228

African (AFR) AF: 0.431 AC: 17845 AN: 41424

American (AMR) AF: 0.649 AC: 9919 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1878 AN: 3470

East Asian (EAS) AF: 0.840 AC: 4316 AN: 5136

South Asian (SAS) AF: 0.623 AC: 3000 AN: 4812

European-Finnish (FIN) AF: 0.528 AC: 5560 AN: 10538

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34995 AN: 67954

Other (OTH) AF: 0.543 AC: 1145 AN: 2108

Alfa AF: 0.527 Hom.: 11825

Bravo AF: 0.531

Asia WGS AF: 0.733 AC: 2551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.44
PhyloP100		-0.39
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: rs7920046; hg19: chr10-123946843;