rs11650989

chr17-61372275-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.2593+3781G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 152,008 control chromosomes in the GnomAD database, including 28,037 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 0.55 (28037 hom., cov: 32)
• Consequence: BCAS3 NM_017679.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.76 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCAS3	NM_017679.5	c.2593+3781G>A		intron_variant		ENST00000407086.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCAS3	ENST00000407086.8	c.2593+3781G>A		intron_variant		1	NM_017679.5	P3
	ENST00000585765.1	n.29-4571C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83659 AN: 151890 Hom.: 28039 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.550 AC: 83665 AN: 152008 Hom.: 28037 Cov.: 32 AF XY: 0.547 AC XY: 40593 AN XY: 74264

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.675

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.773

Gnomad4 NFE AF: 0.766

Gnomad4 OTH AF: 0.562

Alfa AF: 0.701 Hom.: 43483

Bravo AF: 0.509

Asia WGS AF: 0.403 AC: 1404 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.024
Dann	Benign	0.58

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: rs11650989; hg19: chr17-59449636;