NM_017679.5:c.2425+77296A>G

Variant names:

• chr17-61161860-A-G
• rs11868441
• NM_017679.5:c.2425+77296A>G

Variant summary

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

The NM_017679.5(BCAS3):​c.2425+77296A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 152,086 control chromosomes in the GnomAD database, including 35,652 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 0.63 (35652 hom., cov: 32)
• Consequence: BCAS3 NM_017679.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.614
• Publications: 24 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=-0.68).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017679.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCAS3	NM_017679.5	MANE Select	c.2425+77296A>G		intron	N/A	NP_060149.3
	BCAS3	NM_001353144.2		c.2560+77296A>G		intron	N/A	NP_001340073.1
	BCAS3	NM_001330413.2		c.2470+77296A>G		intron	N/A	NP_001317342.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCAS3	ENST00000407086.8	TSL:1 MANE Select	c.2425+77296A>G		intron	N/A	ENSP00000385323.2
	BCAS3	ENST00000390652.9	TSL:1	c.2470+77296A>G		intron	N/A	ENSP00000375067.4
	BCAS3	ENST00000589222.5	TSL:1	c.2425+77296A>G		intron	N/A	ENSP00000466078.1

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95169 AN: 151968 Hom.: 35647 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.740

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.891

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.626 AC: 95175 AN: 152086 Hom.: 35652 Cov.: 32 AF XY: 0.634 AC XY: 47123 AN XY: 74334

African (AFR) AF: 0.179 AC: 7428 AN: 41472

American (AMR) AF: 0.724 AC: 11058 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.740 AC: 2571 AN: 3472

East Asian (EAS) AF: 0.776 AC: 4010 AN: 5166

South Asian (SAS) AF: 0.891 AC: 4297 AN: 4820

European-Finnish (FIN) AF: 0.825 AC: 8727 AN: 10582

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.805 AC: 54763 AN: 67990

Other (OTH) AF: 0.662 AC: 1396 AN: 2108

Alfa AF: 0.743 Hom.: 127042

Bravo AF: 0.596

Asia WGS AF: 0.738 AC: 2568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	12
DANN	Benign	0.63
PhyloP100		0.61
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: rs11868441; hg19: chr17-59239221;