8-38752578-C-T

Variant summary

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

The ENST00000518415.5(TACC1):c.26+7085C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 151,954 control chromosomes in the GnomAD database, including 14,824 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 0.43 (14824 hom., cov: 31)
• Consequence: TACC1 ENST00000518415.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208

Genes affected

TACC1 (HGNC:11522): (transforming acidic coiled-coil containing protein 1) This locus may represent a breast cancer candidate gene. It is located close to FGFR1 on a region of chromosome 8 that is amplified in some breast cancers. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TACC1	NM_001146216.3	c.-425+23907C>T		intron_variant
TACC1	NM_001330521.2	c.-425+23907C>T		intron_variant
TACC1	NM_001352778.2	c.22+10127C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TACC1	ENST00000518415.5	c.26+7085C>T		intron_variant		1
TACC1	ENST00000519416.5	c.-425+23907C>T		intron_variant		1
TACC1	ENST00000520340.5	c.53+10127C>T		intron_variant		5
TACC1	ENST00000520615.5	c.-425+23907C>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65529 AN: 151836 Hom.: 14794 Cov.: 31

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.432 AC: 65593 AN: 151954 Hom.: 14824 Cov.: 31 AF XY: 0.426 AC XY: 31602 AN XY: 74258

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.433

Alfa AF: 0.402 Hom.: 19285

Bravo AF: 0.436

Asia WGS AF: 0.388 AC: 1353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	2.2
Dann	Benign	0.29

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7816768; hg19: chr8-38610096;