chr9-16851680-T-G

Position:

• chr9-16851680-T-G

Variant summary

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

The NM_017637.6(BNC2):​c.3+18966A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 152,018 control chromosomes in the GnomAD database, including 38,868 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 0.71 (38868 hom., cov: 32)
• Consequence: BNC2 NM_017637.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.873

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BNC2	NM_017637.6	c.3+18966A>C		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+18966A>C		intron_variant		2	NM_017637.6	ENSP00000370047.3

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107231 AN: 151900 Hom.: 38860 Cov.: 32

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.766

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.706 AC: 107275 AN: 152018 Hom.: 38868 Cov.: 32 AF XY: 0.712 AC XY: 52928 AN XY: 74288

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.802

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.902

Gnomad4 SAS AF: 0.910

Gnomad4 FIN AF: 0.766

Gnomad4 NFE AF: 0.751

Gnomad4 OTH AF: 0.722

Alfa AF: 0.747 Hom.: 37780

Bravo AF: 0.698

Asia WGS AF: 0.896 AC: 3117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.20
DANN	Benign	0.76

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: rs4961501; hg19: chr9-16851678;