9-16848792-C-T

Position:

• chr9-16848792-C-T

Variant summary

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

The NM_017637.6(BNC2):​c.3+21854G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 151,978 control chromosomes in the GnomAD database, including 21,939 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 0.52 (21939 hom., cov: 32)
• Consequence: BNC2 NM_017637.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BNC2	NM_017637.6	c.3+21854G>A		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+21854G>A		intron_variant		2	NM_017637.6	ENSP00000370047	P2

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79118 AN: 151860 Hom.: 21902 Cov.: 32

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.521 AC: 79211 AN: 151978 Hom.: 21939 Cov.: 32 AF XY: 0.530 AC XY: 39367 AN XY: 74296

Gnomad4 AFR AF: 0.624

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.785

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.534

Alfa AF: 0.474 Hom.: 10158

Bravo AF: 0.536

Asia WGS AF: 0.781 AC: 2714 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.35

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: rs1339552; hg19: chr9-16848790; COSMIC: COSV66143410;