9-16804169-T-G

Position:

• chr9-16804169-T-G

Variant summary

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

The NM_017637.6(BNC2):​c.4-65684A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.495 in 152,214 control chromosomes in the GnomAD database, including 25,066 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 0.49 (25066 hom., cov: 34)
• Consequence: BNC2 NM_017637.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.70

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BNC2	NM_017637.6	c.4-65684A>C		intron_variant		ENST00000380672.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BNC2	ENST00000380672.9	c.4-65684A>C		intron_variant		2	NM_017637.6	P2

Frequencies

GnomAD3 genomes AF: 0.495 AC: 75340 AN: 152096 Hom.: 25068 Cov.: 34

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.00385

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.495 AC: 75331 AN: 152214 Hom.: 25066 Cov.: 34 AF XY: 0.486 AC XY: 36130 AN XY: 74414

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.637

Gnomad4 EAS AF: 0.00386

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.734

Gnomad4 NFE AF: 0.750

Gnomad4 OTH AF: 0.493

Alfa AF: 0.483 Hom.: 2600

Bravo AF: 0.455

Asia WGS AF: 0.114 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.033
DANN	Benign	0.38

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: rs10962612; hg19: chr9-16804167;