rs10887058

Variant names:

• chr10-122054244-A-G
• rs10887058
• NM_206862.4:c.146+3694A>G

Variant summary

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

The NM_206862.4(TACC2):​c.146+3694A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,190 control chromosomes in the GnomAD database, including 5,729 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 0.25 (5729 hom., cov: 33)
• Consequence: TACC2 NM_206862.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.344 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.146+3694A>G		intron	N/A	NP_996744.4
	TACC2	NM_001438364.1		c.206+3694A>G		intron	N/A	NP_001425293.1
	TACC2	NM_001291877.2		c.146+3694A>G		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.146+3694A>G		intron	N/A	ENSP00000358001.1
	TACC2	ENST00000515273.5	TSL:1	c.146+3694A>G		intron	N/A	ENSP00000424467.1
	TACC2	ENST00000515603.5	TSL:1	c.146+3694A>G		intron	N/A	ENSP00000427618.1

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37806 AN: 152072 Hom.: 5724 Cov.: 33

Gnomad AFR AF: 0.0837

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.248 AC: 37817 AN: 152190 Hom.: 5729 Cov.: 33 AF XY: 0.247 AC XY: 18345 AN XY: 74390

African (AFR) AF: 0.0835 AC: 3470 AN: 41552

American (AMR) AF: 0.217 AC: 3323 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 998 AN: 3466

East Asian (EAS) AF: 0.187 AC: 969 AN: 5176

South Asian (SAS) AF: 0.278 AC: 1342 AN: 4824

European-Finnish (FIN) AF: 0.283 AC: 2999 AN: 10590

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23634 AN: 67982

Other (OTH) AF: 0.249 AC: 523 AN: 2100

Alfa AF: 0.295 Hom.: 10143

Bravo AF: 0.233

Asia WGS AF: 0.246 AC: 857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.23
DANN	Benign	0.74
PhyloP100		-2.0
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: rs10887058; hg19: chr10-123813759;