rs9914370

chr17-60945034-A-G

Variant summary

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

The NM_017679.5(BCAS3):c.1088-2185A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,038 control chromosomes in the GnomAD database, including 3,276 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 0.19 (3276 hom., cov: 32)
• Consequence: BCAS3 NM_017679.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCAS3	NM_017679.5	c.1088-2185A>G		intron_variant		ENST00000407086.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCAS3	ENST00000407086.8	c.1088-2185A>G		intron_variant		1	NM_017679.5	P3

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29515 AN: 151920 Hom.: 3267 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.0511

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.194 AC: 29545 AN: 152038 Hom.: 3276 Cov.: 32 AF XY: 0.191 AC XY: 14190 AN XY: 74334

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.0507

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.197

Alfa AF: 0.159 Hom.: 4193

Bravo AF: 0.207

Asia WGS AF: 0.123 AC: 427 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.60
Dann	Benign	0.33

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: rs9914370; hg19: chr17-59022395; COSMIC: COSV66777308;