9-16865701-A-G

Position:

• chr9-16865701-A-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+4945T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,058 control chromosomes in the GnomAD database, including 5,193 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 0.26 (5193 hom., cov: 32)
• Consequence: BNC2 NM_017637.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BNC2	NM_017637.6	c.3+4945T>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+4945T>C		intron_variant		2	NM_017637.6	ENSP00000370047	P2

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39028 AN: 151940 Hom.: 5172 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.0947

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.257 AC: 39092 AN: 152058 Hom.: 5193 Cov.: 32 AF XY: 0.256 AC XY: 19032 AN XY: 74296

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.0940

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.246

Alfa AF: 0.239 Hom.: 2394

Bravo AF: 0.259

Asia WGS AF: 0.228 AC: 790 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.56
DANN	Benign	0.37

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: rs12379183; hg19: chr9-16865699; COSMIC: COSV66143448;