9-16425577-C-T

Position:

• chr9-16425577-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_017637.6(BNC2):​c.2640-5928G>A variant causes a intron change. The variant allele was found at a frequency of 0.093 in 152,138 control chromosomes in the GnomAD database, including 1,873 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 0.093 (1873 hom., cov: 33)
• Consequence: BNC2 NM_017637.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.82

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BNC2	NM_017637.6	c.2640-5928G>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.2640-5928G>A		intron_variant		2	NM_017637.6	ENSP00000370047	P2

Frequencies

GnomAD3 genomes AF: 0.0929 AC: 14118 AN: 152020 Hom.: 1869 Cov.: 33

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0392

Gnomad ASJ AF: 0.00778

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.0531

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00184

Gnomad OTH AF: 0.0680

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

GnomAD4 genome AF: 0.0930 AC: 14152 AN: 152138 Hom.: 1873 Cov.: 33 AF XY: 0.0908 AC XY: 6753 AN XY: 74394

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.0391

Gnomad4 ASJ AF: 0.00778

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.0531

Gnomad4 FIN AF: 0.000283

Gnomad4 NFE AF: 0.00184

Gnomad4 OTH AF: 0.0682

Alfa AF: 0.0345 Hom.: 175

Bravo AF: 0.105

Asia WGS AF: 0.0960 AC: 332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	21
DANN	Benign	0.91

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: rs16934641; hg19: chr9-16425575;