rs11079428

chr17-61389340-T-A

Variant summary

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

The NM_017679.5(BCAS3):c.2594-2637T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 152,532 control chromosomes in the GnomAD database, including 29,700 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 0.59 (29592 hom., cov: 33)
  • Exomes 𝑓: 0.69 (108 hom.)
• Consequence: BCAS3 NM_017679.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCAS3	NM_017679.5	c.2594-2637T>A		intron_variant		ENST00000407086.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCAS3	ENST00000407086.8	c.2594-2637T>A		intron_variant		1	NM_017679.5	P3
	ENST00000585765.1	n.28+10876A>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89926 AN: 151992 Hom.: 29581 Cov.: 33

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.793

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.593

GnomAD4 exome AF: 0.690 AC: 291 AN: 422 Hom.: 108 Cov.: 0 AF XY: 0.694 AC XY: 179 AN XY: 258

Gnomad4 AMR exome AF: 0.350

Gnomad4 ASJ exome AF: 0.00

Gnomad4 SAS exome AF: 0.786

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.726

Gnomad4 OTH exome AF: 0.567

GnomAD4 genome AF: 0.591 AC: 89971 AN: 152110 Hom.: 29592 Cov.: 33 AF XY: 0.587 AC XY: 43677 AN XY: 74354

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.736

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.734

Gnomad4 NFE AF: 0.757

Gnomad4 OTH AF: 0.595

Alfa AF: 0.667 Hom.: 4483

Bravo AF: 0.562

Asia WGS AF: 0.500 AC: 1743 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	0.54
Dann	Benign	0.49

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: rs11079428; hg19: chr17-59466701;