rs798766

Variant names:

• chr4-1732512-T-C
• rs798766
• NM_006342.3:c.1591+1211T>C

Variant summary

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

The NM_006342.3(TACC3):​c.1591+1211T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 151,848 control chromosomes in the GnomAD database, including 44,737 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 0.77 (44737 hom., cov: 35)
• Consequence: TACC3 NM_006342.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 91 publications found

Genes affected

TACC3 (HGNC:11524): (transforming acidic coiled-coil containing protein 3) This gene encodes a member of the transforming acidic colied-coil protein family. The encoded protein is a motor spindle protein that may play a role in stabilization of the mitotic spindle. This protein may also play a role in growth a differentiation of certain cancer cells. [provided by RefSeq, Nov 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TACC3	NM_006342.3	c.1591+1211T>C		intron_variant	Intron 6 of 15	ENST00000313288.9	NP_006333.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TACC3	ENST00000313288.9	c.1591+1211T>C		intron_variant	Intron 6 of 15	1	NM_006342.3	ENSP00000326550.4

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116193 AN: 151734 Hom.: 44689 Cov.: 35

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.812

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.766 AC: 116296 AN: 151848 Hom.: 44737 Cov.: 35 AF XY: 0.764 AC XY: 56673 AN XY: 74198

African (AFR) AF: 0.702 AC: 29028 AN: 41352

American (AMR) AF: 0.722 AC: 11016 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2666 AN: 3462

East Asian (EAS) AF: 0.857 AC: 4427 AN: 5164

South Asian (SAS) AF: 0.791 AC: 3810 AN: 4818

European-Finnish (FIN) AF: 0.770 AC: 8125 AN: 10556

Middle Eastern (MID) AF: 0.759 AC: 220 AN: 290

European-Non Finnish (NFE) AF: 0.805 AC: 54651 AN: 67930

Other (OTH) AF: 0.767 AC: 1616 AN: 2106

Alfa AF: 0.791 Hom.: 159282

Bravo AF: 0.759

Asia WGS AF: 0.828 AC: 2873 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.80
DANN	Benign	0.24
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs798766; hg19: chr4-1734239;