NM_017679.5:c.2426-122467G>A

Variant names:

• chr17-61245860-G-A
• rs7212729
• NM_017679.5:c.2426-122467G>A

Variant summary

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

The NM_017679.5(BCAS3):​c.2426-122467G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.882 in 152,228 control chromosomes in the GnomAD database, including 59,371 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 0.88 (59371 hom., cov: 31)
• Consequence: BCAS3 NM_017679.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152
• Publications: 2 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.92 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BCAS3	NM_017679.5	c.2426-122467G>A		intron_variant	Intron 22 of 23	ENST00000407086.8	NP_060149.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCAS3	ENST00000407086.8	c.2426-122467G>A		intron_variant	Intron 22 of 23	1	NM_017679.5	ENSP00000385323.2

Frequencies

GnomAD3 genomes AF: 0.882 AC: 134206 AN: 152108 Hom.: 59342 Cov.: 31

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.931

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.882 AC: 134293 AN: 152228 Hom.: 59371 Cov.: 31 AF XY: 0.883 AC XY: 65691 AN XY: 74422

African (AFR) AF: 0.928 AC: 38544 AN: 41528

American (AMR) AF: 0.831 AC: 12695 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.824 AC: 2858 AN: 3470

East Asian (EAS) AF: 0.903 AC: 4672 AN: 5176

South Asian (SAS) AF: 0.803 AC: 3870 AN: 4820

European-Finnish (FIN) AF: 0.931 AC: 9874 AN: 10610

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.867 AC: 58974 AN: 68024

Other (OTH) AF: 0.856 AC: 1810 AN: 2114

Alfa AF: 0.866 Hom.: 43608

Bravo AF: 0.879

Asia WGS AF: 0.812 AC: 2823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.4
DANN	Benign	0.72
PhyloP100		-0.15
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: rs7212729; hg19: chr17-59323221;