rs17594273

chr17-60905232-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_017679.5(BCAS3):c.822+2529A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0286 in 152,278 control chromosomes in the GnomAD database, including 83 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 0.029 (83 hom., cov: 32)
• Consequence: BCAS3 NM_017679.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.697

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).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0286 (4349/152278) while in subpopulation NFE AF= 0.0441 (3001/67998). AF 95% confidence interval is 0.0428. There are 83 homozygotes in gnomad4. There are 2061 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 83 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCAS3	NM_017679.5	c.822+2529A>G		intron_variant		ENST00000407086.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCAS3	ENST00000407086.8	c.822+2529A>G		intron_variant		1	NM_017679.5	P3

Frequencies

GnomAD3 genomes AF: 0.0286 AC: 4349 AN: 152160 Hom.: 83 Cov.: 32

Gnomad AFR AF: 0.00704

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0196

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0325

Gnomad FIN AF: 0.0416

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0441

Gnomad OTH AF: 0.0283

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

GnomAD4 genome AF: 0.0286 AC: 4349 AN: 152278 Hom.: 83 Cov.: 32 AF XY: 0.0277 AC XY: 2061 AN XY: 74462

Gnomad4 AFR AF: 0.00702

Gnomad4 AMR AF: 0.0196

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.000963

Gnomad4 SAS AF: 0.0325

Gnomad4 FIN AF: 0.0416

Gnomad4 NFE AF: 0.0441

Gnomad4 OTH AF: 0.0280

Alfa AF: 0.0400 Hom.: 87

Bravo AF: 0.0243

Asia WGS AF: 0.0110 AC: 38 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.9
Dann	Benign	0.39

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: rs17594273; hg19: chr17-58982593;