rs798766

Positions:

• chr4-1732512-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000313288.9(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 ENST00000313288.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
TACC3	NM_006342.3	c.1591+1211T>C		intron_variant		ENST00000313288.9	NP_006333.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TACC3	ENST00000313288.9	c.1591+1211T>C		intron_variant		1	NM_006342.3	ENSP00000326550	P2

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

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.722

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.791

Gnomad4 FIN AF: 0.770

Gnomad4 NFE AF: 0.805

Gnomad4 OTH AF: 0.767

Alfa AF: 0.796 Hom.: 59176

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs798766; hg19: chr4-1734239;