rs9652858

Variant names:

• chr17-61010447-G-A
• rs9652858
• NM_017679.5:c.1487-5304G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017679.5(BCAS3):​c.1487-5304G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,268 control chromosomes in the GnomAD database, including 15,819 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 0.36 (15819 hom., cov: 31)
• Consequence: BCAS3 NM_017679.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.495
• Publications: 6 publications found

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 Gene-Disease associations (from GenCC):

• Hengel-Maroofian-Schols syndrome

  Inheritance: AR Classification: STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCAS3	NM_017679.5	c.1487-5304G>A		intron_variant	Intron 15 of 23	ENST00000407086.8	NP_060149.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCAS3	ENST00000407086.8	c.1487-5304G>A		intron_variant	Intron 15 of 23	1	NM_017679.5	ENSP00000385323.2

Frequencies

GnomAD3 genomes AF: 0.356 AC: 53764 AN: 151158 Hom.: 15758 Cov.: 31

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.0683

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.356 AC: 53875 AN: 151268 Hom.: 15819 Cov.: 31 AF XY: 0.347 AC XY: 25617 AN XY: 73876

African (AFR) AF: 0.815 AC: 33685 AN: 41334

American (AMR) AF: 0.242 AC: 3660 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 708 AN: 3458

East Asian (EAS) AF: 0.135 AC: 698 AN: 5154

South Asian (SAS) AF: 0.0678 AC: 325 AN: 4790

European-Finnish (FIN) AF: 0.163 AC: 1686 AN: 10342

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12182 AN: 67738

Other (OTH) AF: 0.320 AC: 669 AN: 2092

Alfa AF: 0.240 Hom.: 7922

Bravo AF: 0.386

Asia WGS AF: 0.176 AC: 610 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.49
PhyloP100		0.49
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9652858; hg19: chr17-59087808;