rs3861709

Positions:

• chr9-16703102-T-C
• chr9-16703102-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.330+24695A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 152,064 control chromosomes in the GnomAD database, including 29,737 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 0.56 (29737 hom., cov: 32)
• Consequence: BNC2 NM_017637.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.512

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=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BNC2	NM_017637.6	c.330+24695A>G		intron_variant		ENST00000380672.9	NP_060107.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BNC2	ENST00000380672.9	c.330+24695A>G		intron_variant		2	NM_017637.6	ENSP00000370047.3

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84780 AN: 151946 Hom.: 29735 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.767

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.558 AC: 84776 AN: 152064 Hom.: 29737 Cov.: 32 AF XY: 0.553 AC XY: 41080 AN XY: 74342

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.714

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.767

Gnomad4 NFE AF: 0.791

Gnomad4 OTH AF: 0.589

Alfa AF: 0.601 Hom.: 4763

Bravo AF: 0.533

Asia WGS AF: 0.328 AC: 1140 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.1
DANN	Benign	0.89

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: rs3861709; hg19: chr9-16703100;