rs10756815

chr9-16789083-G-Achr9-16789083-G-Cchr9-16789083-G-T

Variant summary

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

The NM_017637.6(BNC2):c.4-50598C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 152,062 control chromosomes in the GnomAD database, including 42,680 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 0.74 (42680 hom., cov: 32)
• Consequence: BNC2 NM_017637.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337

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 = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BNC2	NM_017637.6	c.4-50598C>T		intron_variant		ENST00000380672.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BNC2	ENST00000380672.9	c.4-50598C>T		intron_variant		2	NM_017637.6	P2

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112331 AN: 151944 Hom.: 42666 Cov.: 32

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.849

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.739 AC: 112389 AN: 152062 Hom.: 42680 Cov.: 32 AF XY: 0.733 AC XY: 54505 AN XY: 74336

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.638

Gnomad4 ASJ AF: 0.837

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.825

Gnomad4 NFE AF: 0.849

Gnomad4 OTH AF: 0.757

Alfa AF: 0.818 Hom.: 63971

Bravo AF: 0.718

Asia WGS AF: 0.647 AC: 2254 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.7
Dann	Benign	0.57

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: rs10756815; hg19: chr9-16789081;