17-61379228-C-T

Variant names:

• chr17-61379228-C-T
• rs9895661
• NM_017679.5:c.2593+10734C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_017679.5(BCAS3):​c.2593+10734C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 152,070 control chromosomes in the GnomAD database, including 37,941 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 0.69 (37924 hom., cov: 32)
  • Exomes 𝑓: 0.83 (17 hom.)
• Consequence: BCAS3 NM_017679.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.263
• Publications: 78 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCAS3	NM_017679.5	c.2593+10734C>T		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.2593+10734C>T		intron_variant	Intron 23 of 23	1	NM_017679.5	ENSP00000385323.2

Frequencies

GnomAD3 genomes AF: 0.691 AC: 105036 AN: 151898 Hom.: 37910 Cov.: 32

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.682

GnomAD4 exome AF: 0.827 AC: 43 AN: 52 Hom.: 17 Cov.: 0 AF XY: 0.857 AC XY: 24 AN XY: 28

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 10 AN: 10

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.833 AC: 25 AN: 30

Other (OTH) AF: 0.667 AC: 4 AN: 6

GnomAD4 genome AF: 0.691 AC: 105096 AN: 152018 Hom.: 37924 Cov.: 32 AF XY: 0.684 AC XY: 50835 AN XY: 74312

African (AFR) AF: 0.527 AC: 21815 AN: 41420

American (AMR) AF: 0.570 AC: 8703 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.756 AC: 2625 AN: 3470

East Asian (EAS) AF: 0.484 AC: 2497 AN: 5160

South Asian (SAS) AF: 0.607 AC: 2923 AN: 4816

European-Finnish (FIN) AF: 0.804 AC: 8508 AN: 10588

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.817 AC: 55549 AN: 67978

Other (OTH) AF: 0.684 AC: 1441 AN: 2108

Alfa AF: 0.765 Hom.: 148842

Bravo AF: 0.667

Asia WGS AF: 0.551 AC: 1918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	15
DANN	Benign	0.85
PhyloP100		0.26
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: rs9895661; hg19: chr17-59456589;