rs2254193

chr9-16801852-A-C

Variant summary

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

The NM_017637.6(BNC2):c.4-63367T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0841 in 152,068 control chromosomes in the GnomAD database, including 579 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 0.084 (579 hom., cov: 32)
• Consequence: BNC2 NM_017637.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201

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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BNC2	NM_017637.6	c.4-63367T>G		intron_variant		ENST00000380672.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BNC2	ENST00000380672.9	c.4-63367T>G		intron_variant		2	NM_017637.6	P2

Frequencies

GnomAD3 genomes AF: 0.0841 AC: 12777 AN: 151952 Hom.: 580 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0983

Gnomad ASJ AF: 0.0966

Gnomad EAS AF: 0.00792

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0744

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0696

Gnomad OTH AF: 0.0856

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

GnomAD4 genome AF: 0.0841 AC: 12786 AN: 152068 Hom.: 579 Cov.: 32 AF XY: 0.0842 AC XY: 6257 AN XY: 74350

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.0981

Gnomad4 ASJ AF: 0.0966

Gnomad4 EAS AF: 0.00793

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.0744

Gnomad4 NFE AF: 0.0697

Gnomad4 OTH AF: 0.0851

Alfa AF: 0.0779 Hom.: 322

Bravo AF: 0.0858

Asia WGS AF: 0.0740 AC: 258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.7
Dann	Benign	0.74

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: rs2254193; hg19: chr9-16801850;