rs10124550

Positions:

• chr9-16512750-A-G
• chr9-16512750-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.669+39780T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,222 control chromosomes in the GnomAD database, including 1,250 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 0.11 (1250 hom., cov: 32)
• Consequence: BNC2 NM_017637.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.860

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=-0.51).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BNC2	NM_017637.6	c.669+39780T>C		intron_variant		ENST00000380672.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BNC2	ENST00000380672.9	c.669+39780T>C		intron_variant		2	NM_017637.6	P2

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16867 AN: 152104 Hom.: 1241 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.0628

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0572

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.111 AC: 16909 AN: 152222 Hom.: 1250 Cov.: 32 AF XY: 0.115 AC XY: 8548 AN XY: 74420

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.0628

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0573

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0815 Hom.: 493

Bravo AF: 0.117

Asia WGS AF: 0.210 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	8.5
DANN	Benign	0.80

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: rs10124550; hg19: chr9-16512748;