9-16854369-G-T

Variant names:

• chr9-16854369-G-T
• rs12379687
• NM_017637.6:c.3+16277C>A

Variant summary

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

The NM_017637.6(BNC2):​c.3+16277C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,078 control chromosomes in the GnomAD database, including 1,146 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 0.11 (1146 hom., cov: 32)
• Consequence: BNC2 NM_017637.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BNC2	NM_017637.6	c.3+16277C>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.3+16277C>A		intron_variant	Intron 1 of 6	2	NM_017637.6	ENSP00000370047.3

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16382 AN: 151960 Hom.: 1144 Cov.: 32

Gnomad AFR AF: 0.0264

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.0829

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0570

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.0995

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

GnomAD4 genome AF: 0.108 AC: 16381 AN: 152078 Hom.: 1146 Cov.: 32 AF XY: 0.106 AC XY: 7890 AN XY: 74328

Gnomad4 AFR AF: 0.0263

Gnomad4 AMR AF: 0.0827

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0578

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.0980

Alfa AF: 0.125 Hom.: 862

Bravo AF: 0.0970

Asia WGS AF: 0.0290 AC: 102 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.087
DANN	Benign	0.63

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: rs12379687; hg19: chr9-16854367; COSMIC: COSV66143422;