10-122097918-A-G

Variant names:

• chr10-122097918-A-G
• rs2420992
• NM_206862.4:c.5573+9327A>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.5573+9327A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 151,932 control chromosomes in the GnomAD database, including 24,996 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 0.57 (24996 hom., cov: 32)
• Consequence: TACC2 NM_206862.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.243
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.683 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.5573+9327A>G		intron	N/A	NP_996744.4	O95359-4
	TACC2	NM_001438364.1		c.5633+9327A>G		intron	N/A	NP_001425293.1
	TACC2	NM_001291877.2		c.5720+9180A>G		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.5573+9327A>G		intron	N/A	ENSP00000358001.1	O95359-4
	TACC2	ENST00000515273.5	TSL:1	c.5720+9180A>G		intron	N/A	ENSP00000424467.1	E9PBC6
	TACC2	ENST00000515603.5	TSL:1	c.5573+9327A>G		intron	N/A	ENSP00000427618.1	E7EMZ9

Frequencies

GnomAD3 genomes AF: 0.573 AC: 86970 AN: 151814 Hom.: 24967 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.573 AC: 87051 AN: 151932 Hom.: 24996 Cov.: 32 AF XY: 0.571 AC XY: 42420 AN XY: 74246

African (AFR) AF: 0.597 AC: 24749 AN: 41438

American (AMR) AF: 0.564 AC: 8626 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1985 AN: 3472

East Asian (EAS) AF: 0.702 AC: 3601 AN: 5126

South Asian (SAS) AF: 0.589 AC: 2829 AN: 4802

European-Finnish (FIN) AF: 0.502 AC: 5304 AN: 10558

Middle Eastern (MID) AF: 0.607 AC: 176 AN: 290

European-Non Finnish (NFE) AF: 0.558 AC: 37935 AN: 67942

Other (OTH) AF: 0.608 AC: 1284 AN: 2112

Alfa AF: 0.572 Hom.: 45823

Bravo AF: 0.579

Asia WGS AF: 0.643 AC: 2239 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.1
DANN	Benign	0.68
PhyloP100		0.24
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: rs2420992; hg19: chr10-123857433;