17-61286621-C-T

Position:

• chr17-61286621-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017679.5(BCAS3):​c.2426-81706C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,036 control chromosomes in the GnomAD database, including 1,222 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 0.12 (1222 hom., cov: 32)
• Consequence: BCAS3 NM_017679.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

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=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BCAS3	NM_017679.5	c.2426-81706C>T		intron_variant		ENST00000407086.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCAS3	ENST00000407086.8	c.2426-81706C>T		intron_variant		1	NM_017679.5	P3

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18982 AN: 151918 Hom.: 1218 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.0799

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.125 AC: 18990 AN: 152036 Hom.: 1222 Cov.: 32 AF XY: 0.123 AC XY: 9144 AN XY: 74316

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.0799

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.140

Alfa AF: 0.0979 Hom.: 230

Bravo AF: 0.127

Asia WGS AF: 0.178 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	1.8
DANN	Benign	0.64

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: rs4968551; hg19: chr17-59363982;