rs2079742

Variant names:

• chr17-61388336-T-C
• rs2079742
• NM_017679.5:c.2594-3641T>C

Variant summary

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

The NM_017679.5(BCAS3):​c.2594-3641T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 388,468 control chromosomes in the GnomAD database, including 10,691 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 0.20 (3954 hom., cov: 31)
  • Exomes 𝑓: 0.20 (6737 hom.)
• Consequence: BCAS3 NM_017679.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276
• Publications: 32 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]

TBX2-AS1 (HGNC:50355): (TBX2 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.483 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCAS3	NM_017679.5	c.2594-3641T>C		intron_variant	Intron 23 of 23	ENST00000407086.8	NP_060149.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCAS3	ENST00000407086.8	c.2594-3641T>C		intron_variant	Intron 23 of 23	1	NM_017679.5	ENSP00000385323.2

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30819 AN: 151798 Hom.: 3954 Cov.: 31

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.232

GnomAD4 exome AF: 0.204 AC: 48162 AN: 236554 Hom.: 6737 Cov.: 0 AF XY: 0.213 AC XY: 26522 AN XY: 124550

African (AFR) AF: 0.165 AC: 1176 AN: 7142

American (AMR) AF: 0.425 AC: 3927 AN: 9234

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 1279 AN: 7238

East Asian (EAS) AF: 0.493 AC: 7142 AN: 14498

South Asian (SAS) AF: 0.334 AC: 8914 AN: 26680

European-Finnish (FIN) AF: 0.174 AC: 2323 AN: 13324

Middle Eastern (MID) AF: 0.225 AC: 229 AN: 1020

European-Non Finnish (NFE) AF: 0.143 AC: 20569 AN: 143852

Other (OTH) AF: 0.192 AC: 2603 AN: 13566

GnomAD4 genome AF: 0.203 AC: 30825 AN: 151914 Hom.: 3954 Cov.: 31 AF XY: 0.215 AC XY: 15987 AN XY: 74228

African (AFR) AF: 0.174 AC: 7207 AN: 41440

American (AMR) AF: 0.372 AC: 5673 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 609 AN: 3470

East Asian (EAS) AF: 0.500 AC: 2557 AN: 5118

South Asian (SAS) AF: 0.369 AC: 1770 AN: 4792

European-Finnish (FIN) AF: 0.192 AC: 2029 AN: 10580

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10350 AN: 67950

Other (OTH) AF: 0.233 AC: 489 AN: 2102

Alfa AF: 0.190 Hom.: 3206

Bravo AF: 0.214

Asia WGS AF: 0.413 AC: 1431 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	3.3
DANN	Benign	0.54
PhyloP100		-0.28
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: rs2079742; hg19: chr17-59465697;