9-16789880-C-T

Variant names:

• chr9-16789880-C-T
• rs4961760
• NM_017637.6:c.4-51395G>A

Variant summary

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

The NM_017637.6(BNC2):​c.4-51395G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.878 in 152,220 control chromosomes in the GnomAD database, including 58,933 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 0.88 (58933 hom., cov: 33)
• Consequence: BNC2 NM_017637.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BNC2	NM_017637.6	c.4-51395G>A		intron_variant	Intron 1 of 6	ENST00000380672.9	NP_060107.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BNC2	ENST00000380672.9	c.4-51395G>A		intron_variant	Intron 1 of 6	2	NM_017637.6	ENSP00000370047.3

Frequencies

GnomAD3 genomes AF: 0.878 AC: 133604 AN: 152102 Hom.: 58892 Cov.: 33

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.915

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.925

Gnomad OTH AF: 0.878

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

GnomAD4 genome AF: 0.878 AC: 133703 AN: 152220 Hom.: 58933 Cov.: 33 AF XY: 0.878 AC XY: 65380 AN XY: 74430

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.890

Gnomad4 ASJ AF: 0.915

Gnomad4 EAS AF: 0.877

Gnomad4 SAS AF: 0.841

Gnomad4 FIN AF: 0.918

Gnomad4 NFE AF: 0.925

Gnomad4 OTH AF: 0.877

Alfa AF: 0.913 Hom.: 62089

Bravo AF: 0.872

Asia WGS AF: 0.841 AC: 2927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.61

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: rs4961760; hg19: chr9-16789878;