rs2079742

Positions:

• chr17-61388336-T-C

Variant summary

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

The NM_017679.5(BCAS3):​c.2594-3641T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 388,468 control chromosomes in the GnomAD database, including 10,691 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 0.20 (3954 hom., cov: 31)
  • Exomes 𝑓: 0.20 (6737 hom.)
• Consequence: BCAS3 NM_017679.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

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]

BCAS3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BCAS3	NM_017679.5	c.2594-3641T>C		intron_variant		ENST00000407086.8	NP_060149.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BCAS3	ENST00000407086.8	c.2594-3641T>C		intron_variant		1	NM_017679.5	ENSP00000385323.2

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30819 AN: 151798 Hom.: 3954 Cov.: 31

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.232

GnomAD4 exome AF: 0.204 AC: 48162 AN: 236554 Hom.: 6737 Cov.: 0 AF XY: 0.213 AC XY: 26522 AN XY: 124550

Gnomad4 AFR exome AF: 0.165

Gnomad4 AMR exome AF: 0.425

Gnomad4 ASJ exome AF: 0.177

Gnomad4 EAS exome AF: 0.493

Gnomad4 SAS exome AF: 0.334

Gnomad4 FIN exome AF: 0.174

Gnomad4 NFE exome AF: 0.143

Gnomad4 OTH exome AF: 0.192

GnomAD4 genome AF: 0.203 AC: 30825 AN: 151914 Hom.: 3954 Cov.: 31 AF XY: 0.215 AC XY: 15987 AN XY: 74228

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.500

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.233

Alfa AF: 0.179 Hom.: 1673

Bravo AF: 0.214

Asia WGS AF: 0.413 AC: 1431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.3
DANN	Benign	0.54

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: rs2079742; hg19: chr17-59465697;