chr9-16858086-G-A

Position:

• chr9-16858086-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_017637.6(BNC2):​c.3+12560C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 152,050 control chromosomes in the GnomAD database, including 23,155 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 0.51 (23155 hom., cov: 33)
• Consequence: BNC2 NM_017637.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BNC2	NM_017637.6	c.3+12560C>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+12560C>T		intron_variant		2	NM_017637.6	ENSP00000370047	P2

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76904 AN: 151934 Hom.: 23150 Cov.: 33

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.506 AC: 76906 AN: 152050 Hom.: 23155 Cov.: 33 AF XY: 0.510 AC XY: 37927 AN XY: 74334

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.567

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.542

Gnomad4 SAS AF: 0.562

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.536

Alfa AF: 0.640 Hom.: 61318

Bravo AF: 0.484

Asia WGS AF: 0.505 AC: 1758 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	15
DANN	Benign	0.69

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: rs10756819; hg19: chr9-16858084;