chr8-38738877-G-A

Position:

• chr8-38738877-G-A

Variant summary

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

The NM_001352778.2(TACC1):​c.-79-3474G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 151,842 control chromosomes in the GnomAD database, including 33,508 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 0.66 (33508 hom., cov: 30)
• Consequence: TACC1 NM_001352778.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.666

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]

TACC1 (HGNC:):

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 = 0.93 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TACC1	NM_001352778.2	c.-79-3474G>A		intron_variant			NP_001339707.1
TACC1	NM_001352780.2	c.-79-3474G>A		intron_variant			NP_001339709.1
TACC1	NM_001352787.2	c.-48-3474G>A		intron_variant			NP_001339716.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TACC1	ENST00000518415.5	c.-674-3474G>A		intron_variant		1		ENSP00000428706.1
TACC1	ENST00000519416.5	c.-425+10206G>A		intron_variant		1		ENSP00000428687.1
TACC1	ENST00000520615.5	c.-425+10206G>A		intron_variant		2		ENSP00000428450.1

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100104 AN: 151724 Hom.: 33474 Cov.: 30

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.952

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.660 AC: 100194 AN: 151842 Hom.: 33508 Cov.: 30 AF XY: 0.665 AC XY: 49341 AN XY: 74200

Gnomad4 AFR AF: 0.706

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.952

Gnomad4 SAS AF: 0.740

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.612

Alfa AF: 0.611 Hom.: 35217

Bravo AF: 0.657

Asia WGS AF: 0.837 AC: 2910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.31
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4733947; hg19: chr8-38596395;