8-38738877-G-T

Variant names:

• chr8-38738877-G-T
• rs4733947
• ENST00000518415.5:c.-674-3474G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000518415.5(TACC1):​c.-674-3474G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
• Consequence: TACC1 ENST00000518415.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.666
• Publications: 2 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TACC1	NM_001352778.2	c.-79-3474G>T		intron_variant	Intron 1 of 14		NP_001339707.1
TACC1	NM_001352780.2	c.-79-3474G>T		intron_variant	Intron 1 of 14		NP_001339709.1
TACC1	NM_001352787.2	c.-48-3474G>T		intron_variant	Intron 1 of 13		NP_001339716.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TACC1	ENST00000518415.5	c.-674-3474G>T		intron_variant	Intron 1 of 14	1		ENSP00000428706.1
TACC1	ENST00000519416.5	c.-425+10206G>T		intron_variant	Intron 1 of 12	1		ENSP00000428687.1
TACC1	ENST00000520615.5	c.-425+10206G>T		intron_variant	Intron 1 of 12	2		ENSP00000428450.1

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 45926

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.24
DANN	Benign	0.51
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs4733947; hg19: chr8-38596395;