rs1029015

chr9-16657398-A-Cchr9-16657398-A-Gchr9-16657398-A-T

Variant summary

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

The NM_017637.6(BNC2):c.330+70399T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 152,098 control chromosomes in the GnomAD database, including 18,414 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 0.46 (18414 hom., cov: 32)
• Consequence: BNC2 NM_017637.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BNC2	NM_017637.6	c.330+70399T>G		intron_variant		ENST00000380672.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BNC2	ENST00000380672.9	c.330+70399T>G		intron_variant		2	NM_017637.6	P2

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70316 AN: 151980 Hom.: 18412 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.462 AC: 70325 AN: 152098 Hom.: 18414 Cov.: 32 AF XY: 0.463 AC XY: 34446 AN XY: 74330

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.688

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.525

Alfa AF: 0.511 Hom.: 2657

Bravo AF: 0.463

Asia WGS AF: 0.500 AC: 1741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.0060
Dann	Benign	0.53

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: rs1029015; hg19: chr9-16657396;