chr9-16789438-G-A

Position:

• chr9-16789438-G-A

Variant summary

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

The NM_017637.6(BNC2):​c.4-50953C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 152,078 control chromosomes in the GnomAD database, including 54,721 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 0.84 (54721 hom., cov: 31)
• Consequence: BNC2 NM_017637.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BNC2	NM_017637.6	c.4-50953C>T		intron_variant		ENST00000380672.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BNC2	ENST00000380672.9	c.4-50953C>T		intron_variant		2	NM_017637.6	P2

Frequencies

GnomAD3 genomes AF: 0.842 AC: 127989 AN: 151960 Hom.: 54694 Cov.: 31

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.915

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.924

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.842 AC: 128068 AN: 152078 Hom.: 54721 Cov.: 31 AF XY: 0.842 AC XY: 62578 AN XY: 74312

Gnomad4 AFR AF: 0.687

Gnomad4 AMR AF: 0.853

Gnomad4 ASJ AF: 0.915

Gnomad4 EAS AF: 0.746

Gnomad4 SAS AF: 0.833

Gnomad4 FIN AF: 0.918

Gnomad4 NFE AF: 0.924

Gnomad4 OTH AF: 0.846

Alfa AF: 0.888 Hom.: 26209

Bravo AF: 0.826

Asia WGS AF: 0.787 AC: 2741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.9
DANN	Benign	0.81

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: rs6475082; hg19: chr9-16789436;