rs139961894

Variant names:

• chr17-61034748-A-C
• rs139961894
• NM_017679.5:c.1720A>C

Your query was ambiguous. Multiple possible variants found:

• chr17-61034748-A-C
• chr17-61034748-A-G

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Moderate BP6_Moderate BP7 BS1 BS2

The NM_017679.5(BCAS3):​c.1720A>C​(p.Arg574Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00689 in 1,612,952 control chromosomes in the GnomAD database, including 45 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0053 (1 hom., cov: 32)
  • Exomes 𝑓: 0.0071 (44 hom.)
• Consequence: BCAS3 NM_017679.5 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 3.06
• 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-AS1 (HGNC:56376): (BCAS3 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BP6: Variant 17-61034748-A-C is Benign according to our data. Variant chr17-61034748-A-C is described in ClinVar as Likely_benign. ClinVar VariationId is 2647996.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=3.06 with no splicing effect.
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.00529 (805/152308) while in subpopulation NFE AF = 0.0081 (551/68020). AF 95% confidence interval is 0.00754. There are 1 homozygotes in GnomAd4. There are 411 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAdExome4 at 44 AR gene

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCAS3	NM_017679.5	MANE Select	c.1720A>C	p.Arg574Arg	synonymous	Exon 17 of 24	NP_060149.3
	BCAS3	NM_001353144.2		c.1855A>C	p.Arg619Arg	synonymous	Exon 19 of 26	NP_001340073.1
	BCAS3	NM_001330413.2		c.1765A>C	p.Arg589Arg	synonymous	Exon 18 of 26	NP_001317342.1	Q9H6U6-8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCAS3	ENST00000407086.8	TSL:1 MANE Select	c.1720A>C	p.Arg574Arg	synonymous	Exon 17 of 24	ENSP00000385323.2	Q9H6U6-2
	BCAS3	ENST00000390652.9	TSL:1	c.1765A>C	p.Arg589Arg	synonymous	Exon 18 of 25	ENSP00000375067.4	Q9H6U6-1
	BCAS3	ENST00000589222.5	TSL:1	c.1720A>C	p.Arg574Arg	synonymous	Exon 17 of 26	ENSP00000466078.1	Q9H6U6-7

Frequencies

GnomAD3 genomes AF: 0.00529 AC: 805 AN: 152190 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.00118

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00327

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00352

Gnomad FIN AF: 0.0121

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00810

Gnomad OTH AF: 0.00334

GnomAD2 exomes AF: 0.00481 AC: 1195 AN: 248578 AF XY: 0.00471

Gnomad AFR exome AF: 0.000907

Gnomad AMR exome AF: 0.00146

Gnomad ASJ exome AF: 0.00120

Gnomad EAS exome AF: 0.000112

Gnomad FIN exome AF: 0.0110

Gnomad NFE exome AF: 0.00692

Gnomad OTH exome AF: 0.00563

GnomAD4 exome AF: 0.00706 AC: 10307 AN: 1460644 Hom.: 44 Cov.: 30 AF XY: 0.00684 AC XY: 4971 AN XY: 726692

African (AFR) AF: 0.000808 AC: 27 AN: 33416

American (AMR) AF: 0.00123 AC: 55 AN: 44620

Ashkenazi Jewish (ASJ) AF: 0.000728 AC: 19 AN: 26088

East Asian (EAS) AF: 0.0000252 AC: 1 AN: 39624

South Asian (SAS) AF: 0.00177 AC: 152 AN: 86042

European-Finnish (FIN) AF: 0.0107 AC: 572 AN: 53414

Middle Eastern (MID) AF: 0.00139 AC: 8 AN: 5762

European-Non Finnish (NFE) AF: 0.00818 AC: 9087 AN: 1111334

Other (OTH) AF: 0.00640 AC: 386 AN: 60344

GnomAD4 genome AF: 0.00529 AC: 805 AN: 152308 Hom.: 1 Cov.: 32 AF XY: 0.00552 AC XY: 411 AN XY: 74476

African (AFR) AF: 0.00118 AC: 49 AN: 41572

American (AMR) AF: 0.00327 AC: 50 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.000576 AC: 2 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5182

South Asian (SAS) AF: 0.00352 AC: 17 AN: 4824

European-Finnish (FIN) AF: 0.0121 AC: 128 AN: 10616

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00810 AC: 551 AN: 68020

Other (OTH) AF: 0.00331 AC: 7 AN: 2116

Alfa AF: 0.00612 Hom.: 4

Bravo AF: 0.00426

EpiCase AF: 0.00736

EpiControl AF: 0.00612

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	17
DANN	Benign	0.68
PhyloP100		3.1
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs139961894; hg19: chr17-59112109;