rs6504016

Variant names:

• chr17-61080882-G-A
• rs6504016
• NM_017679.5:c.2327+2353G>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.2327+2353G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.947 in 152,324 control chromosomes in the GnomAD database, including 68,409 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 0.95 (68409 hom., cov: 33)
• Consequence: BCAS3 NM_017679.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.54
• Publications: 2 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-AS1 (HGNC:56376): (BCAS3 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCAS3	NM_017679.5	c.2327+2353G>A		intron_variant	Intron 21 of 23	ENST00000407086.8	NP_060149.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCAS3	ENST00000407086.8	c.2327+2353G>A		intron_variant	Intron 21 of 23	1	NM_017679.5	ENSP00000385323.2

Frequencies

GnomAD3 genomes AF: 0.947 AC: 144156 AN: 152206 Hom.: 68345 Cov.: 33

Gnomad AFR AF: 0.985

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.935

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.927

Gnomad OTH AF: 0.935

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

GnomAD4 genome AF: 0.947 AC: 144278 AN: 152324 Hom.: 68409 Cov.: 33 AF XY: 0.947 AC XY: 70545 AN XY: 74488

African (AFR) AF: 0.985 AC: 40968 AN: 41576

American (AMR) AF: 0.935 AC: 14299 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.922 AC: 3201 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5187 AN: 5190

South Asian (SAS) AF: 0.966 AC: 4664 AN: 4826

European-Finnish (FIN) AF: 0.927 AC: 9841 AN: 10614

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.927 AC: 63050 AN: 68026

Other (OTH) AF: 0.935 AC: 1978 AN: 2116

Alfa AF: 0.928 Hom.: 107577

Bravo AF: 0.948

Asia WGS AF: 0.983 AC: 3416 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.39
PhyloP100		-2.5
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: rs6504016; hg19: chr17-59158243;