rs17103129

Variant names:

• chr10-122150884-T-C
• rs17103129
• NM_206862.4:c.5834+7178T>C

Variant summary

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

The NM_206862.4(TACC2):​c.5834+7178T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0392 in 152,268 control chromosomes in the GnomAD database, including 216 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 0.039 (216 hom., cov: 32)
• Consequence: TACC2 NM_206862.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.353
• Publications: 3 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]

ENSG00000285973 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.159 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACC2	NM_206862.4	MANE Select	c.5834+7178T>C		intron	N/A	NP_996744.4	O95359-4
	TACC2	NM_001438364.1		c.5759+18150T>C		intron	N/A	NP_001425293.1
	TACC2	NM_001291877.2		c.5846+18150T>C		intron	N/A	NP_001278806.2	E9PBC6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACC2	ENST00000369005.6	TSL:1 MANE Select	c.5834+7178T>C		intron	N/A	ENSP00000358001.1	O95359-4
	TACC2	ENST00000515273.5	TSL:1	c.5846+18150T>C		intron	N/A	ENSP00000424467.1	E9PBC6
	TACC2	ENST00000515603.5	TSL:1	c.5699+18150T>C		intron	N/A	ENSP00000427618.1	E7EMZ9

Frequencies

GnomAD3 genomes AF: 0.0392 AC: 5970 AN: 152150 Hom.: 216 Cov.: 32

Gnomad AFR AF: 0.00915

Gnomad AMI AF: 0.0473

Gnomad AMR AF: 0.0522

Gnomad ASJ AF: 0.0415

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.0477

Gnomad FIN AF: 0.0412

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0436

Gnomad OTH AF: 0.0420

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

GnomAD4 genome AF: 0.0392 AC: 5970 AN: 152268 Hom.: 216 Cov.: 32 AF XY: 0.0404 AC XY: 3006 AN XY: 74434

African (AFR) AF: 0.00912 AC: 379 AN: 41564

American (AMR) AF: 0.0522 AC: 799 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0415 AC: 144 AN: 3468

East Asian (EAS) AF: 0.168 AC: 868 AN: 5154

South Asian (SAS) AF: 0.0477 AC: 230 AN: 4818

European-Finnish (FIN) AF: 0.0412 AC: 437 AN: 10616

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0436 AC: 2967 AN: 68020

Other (OTH) AF: 0.0421 AC: 89 AN: 2116

Alfa AF: 0.0436 Hom.: 250

Bravo AF: 0.0391

Asia WGS AF: 0.0850 AC: 294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.2
DANN	Benign	0.72
PhyloP100		0.35
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: rs17103129; hg19: chr10-123910399;