8-38752578-C-T

Variant names:

• chr8-38752578-C-T
• rs7816768
• ENST00000518415.5:c.26+7085C>T

Variant summary

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

The NM_001352778.2(TACC1):​c.22+10127C>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 NM_001352778.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208
• Publications: 9 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: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001352778.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACC1	NM_001352778.2		c.22+10127C>T		intron	N/A	NP_001339707.1
	TACC1	NM_001352780.2		c.22+10127C>T		intron	N/A	NP_001339709.1
	TACC1	NM_001352787.2		c.53+10127C>T		intron	N/A	NP_001339716.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TACC1	ENST00000518415.5	TSL:1	c.26+7085C>T		intron	N/A	ENSP00000428706.1
	TACC1	ENST00000519416.5	TSL:1	c.-425+23907C>T		intron	N/A	ENSP00000428687.1
	TACC1	ENST00000885325.1		c.-27+23907C>T		intron	N/A	ENSP00000555384.1

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

African (AFR) AF: 0.567 AC: 23485 AN: 41420

American (AMR) AF: 0.322 AC: 4921 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1858 AN: 3468

East Asian (EAS) AF: 0.298 AC: 1540 AN: 5172

South Asian (SAS) AF: 0.415 AC: 1998 AN: 4818

European-Finnish (FIN) AF: 0.327 AC: 3451 AN: 10538

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26994 AN: 67948

Other (OTH) AF: 0.433 AC: 913 AN: 2110

Alfa AF: 0.407 Hom.: 46218

Bravo AF: 0.436

Asia WGS AF: 0.388 AC: 1353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.2
DANN	Benign	0.29
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs7816768; hg19: chr8-38610096;