chr10-122153815-T-C

Variant names:

• chr10-122153815-T-C
• rs17103138
• NM_206862.4:c.5834+10109T>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+10109T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,266 control chromosomes in the GnomAD database, including 1,383 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 0.12 (1383 hom., cov: 32)
• Consequence: TACC2 NM_206862.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 11 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]

LOC124902518 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TACC2	NM_206862.4	c.5834+10109T>C		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.5834+10109T>C		intron_variant	Intron 7 of 22	1	NM_206862.4	ENSP00000358001.1

Frequencies

GnomAD3 genomes AF: 0.118 AC: 18023 AN: 152148 Hom.: 1382 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0851

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0845

Gnomad SAS AF: 0.0728

Gnomad FIN AF: 0.0833

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.0816

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.119 AC: 18052 AN: 152266 Hom.: 1383 Cov.: 32 AF XY: 0.116 AC XY: 8648 AN XY: 74446

African (AFR) AF: 0.212 AC: 8787 AN: 41534

American (AMR) AF: 0.0850 AC: 1301 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 392 AN: 3470

East Asian (EAS) AF: 0.0845 AC: 438 AN: 5186

South Asian (SAS) AF: 0.0726 AC: 350 AN: 4818

European-Finnish (FIN) AF: 0.0833 AC: 884 AN: 10610

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.0816 AC: 5550 AN: 68028

Other (OTH) AF: 0.123 AC: 260 AN: 2112

Alfa AF: 0.0963 Hom.: 2900

Bravo AF: 0.124

Asia WGS AF: 0.0940 AC: 328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.7
DANN	Benign	0.74
PhyloP100		0.057
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs17103138; hg19: chr10-123913330;