rs10756815

Variant names:

• chr9-16789083-G-A
• rs10756815
• NM_017637.6:c.4-50598C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-16789083-G-A
• chr9-16789083-G-C
• chr9-16789083-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

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]

BNC2 Gene-Disease associations (from GenCC):

• lower urinary tract obstruction, congenital

  Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
• posterior urethral valve

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
BNC2	NM_017637.6	c.4-50598C>T		intron_variant	Intron 1 of 6	ENST00000380672.9	NP_060107.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BNC2	ENST00000380672.9	c.4-50598C>T		intron_variant	Intron 1 of 6	2	NM_017637.6	ENSP00000370047.3

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

African (AFR) AF: 0.595 AC: 24626 AN: 41416

American (AMR) AF: 0.638 AC: 9754 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.837 AC: 2903 AN: 3470

East Asian (EAS) AF: 0.557 AC: 2875 AN: 5164

South Asian (SAS) AF: 0.652 AC: 3138 AN: 4816

European-Finnish (FIN) AF: 0.825 AC: 8730 AN: 10584

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.849 AC: 57766 AN: 68006

Other (OTH) AF: 0.757 AC: 1601 AN: 2116

Alfa AF: 0.807 Hom.: 80514

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
PhyloP100		-0.34
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10756815; hg19: chr9-16789081;