rs1416742

Positions:

• chr9-16856885-G-A
• chr9-16856885-G-T

Variant summary

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

The NM_017637.6(BNC2):​c.3+13761C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 151,986 control chromosomes in the GnomAD database, including 16,256 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 0.42 (16256 hom., cov: 31)
• Consequence: BNC2 NM_017637.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68

Genes affected

BNC2 (HGNC:30988): (basonuclin zinc finger protein 2) This gene encodes a conserved zinc finger protein. The encoded protein functions in skin color saturation. Mutations in this gene are associated with facial pigmented spots. This gene is also associated with susceptibility to adolescent idiopathic scoliosis. [provided by RefSeq, Jul 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BNC2	NM_017637.6	c.3+13761C>T		intron_variant		ENST00000380672.9	NP_060107.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BNC2	ENST00000380672.9	c.3+13761C>T		intron_variant		2	NM_017637.6	ENSP00000370047.3

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64403 AN: 151866 Hom.: 16258 Cov.: 31

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.424 AC: 64400 AN: 151986 Hom.: 16256 Cov.: 31 AF XY: 0.418 AC XY: 31032 AN XY: 74272

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.470

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.584

Gnomad4 OTH AF: 0.422

Alfa AF: 0.464 Hom.: 4787

Bravo AF: 0.402

Asia WGS AF: 0.212 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	11
DANN	Benign	0.84

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: rs1416742; hg19: chr9-16856883;