rs7860932

chr9-16786900-G-Achr9-16786900-G-Cchr9-16786900-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.4-48415C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.885 in 152,156 control chromosomes in the GnomAD database, including 59,599 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 0.88 (59599 hom., cov: 32)
• Consequence: BNC2 NM_017637.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.503

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BNC2	NM_017637.6	c.4-48415C>T		intron_variant		ENST00000380672.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BNC2	ENST00000380672.9	c.4-48415C>T		intron_variant		2	NM_017637.6	P2

Frequencies

GnomAD3 genomes AF: 0.885 AC: 134524 AN: 152038 Hom.: 59553 Cov.: 32

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.941

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.903

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.886

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

GnomAD4 genome AF: 0.885 AC: 134627 AN: 152156 Hom.: 59599 Cov.: 32 AF XY: 0.883 AC XY: 65667 AN XY: 74376

Gnomad4 AFR AF: 0.852

Gnomad4 AMR AF: 0.882

Gnomad4 ASJ AF: 0.916

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.829

Gnomad4 FIN AF: 0.903

Gnomad4 NFE AF: 0.911

Gnomad4 OTH AF: 0.885

Alfa AF: 0.901 Hom.: 58862

Bravo AF: 0.881

Asia WGS AF: 0.795 AC: 2767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	2.3
Dann	Benign	0.56

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: rs7860932; hg19: chr9-16786898;