rs9303437

Positions:

• chr17-61058454-C-T

Variant summary

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

The NM_017679.5(BCAS3):​c.2030-16466C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,060 control chromosomes in the GnomAD database, including 2,559 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 0.18 (2559 hom., cov: 31)
• Consequence: BCAS3 NM_017679.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.379

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-AS1 (HGNC:56376): (BCAS3 antisense RNA 1)

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 (AFR) allele frequency at 95% confidence interval = 0.219 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCAS3	NM_017679.5	c.2030-16466C>T		intron_variant		ENST00000407086.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCAS3	ENST00000407086.8	c.2030-16466C>T		intron_variant		1	NM_017679.5	P3
BCAS3-AS1	ENST00000588604.1	n.118+11551G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27048 AN: 151940 Hom.: 2555 Cov.: 31

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.0429

Gnomad SAS AF: 0.0366

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.178 AC: 27057 AN: 152060 Hom.: 2559 Cov.: 31 AF XY: 0.174 AC XY: 12915 AN XY: 74324

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.0430

Gnomad4 SAS AF: 0.0369

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.193

Alfa AF: 0.174 Hom.: 1126

Bravo AF: 0.184

Asia WGS AF: 0.0590 AC: 207 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	2.5
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: rs9303437; hg19: chr17-59135815;