rs3902107

Positions:

• chr17-61310649-G-A

Variant summary

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

The NM_017679.5(BCAS3):​c.2426-57678G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 151,978 control chromosomes in the GnomAD database, including 7,515 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 0.27 (7515 hom., cov: 32)
• Consequence: BCAS3 NM_017679.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.286

Genes affected

BCAS3 (HGNC:14347): (BCAS3 microtubule associated cell migration factor) Enables several functions, including acetyltransferase activator activity; beta-tubulin binding activity; and histone acetyltransferase binding activity. Involved in cellular response to estrogen stimulus; positive regulation of catalytic activity; and positive regulation of transcription by RNA polymerase II. Located in nucleus; phagophore assembly site; and transcriptionally active chromatin. Biomarker of breast cancer. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCAS3	NM_017679.5	c.2426-57678G>A		intron_variant		ENST00000407086.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCAS3	ENST00000407086.8	c.2426-57678G>A		intron_variant		1	NM_017679.5	P3

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40759 AN: 151866 Hom.: 7500 Cov.: 32

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.269 AC: 40809 AN: 151978 Hom.: 7515 Cov.: 32 AF XY: 0.266 AC XY: 19728 AN XY: 74266

Gnomad4 AFR AF: 0.525

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.241

Alfa AF: 0.173 Hom.: 3707

Bravo AF: 0.289

Asia WGS AF: 0.174 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.8
DANN	Benign	0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs3902107; hg19: chr17-59388010;