rs6475082

Variant names:

• chr9-16789438-G-A
• rs6475082
• NM_017637.6:c.4-50953C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-16789438-G-A
• chr9-16789438-G-C
• chr9-16789438-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.4-50953C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 152,078 control chromosomes in the GnomAD database, including 54,721 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 0.84 (54721 hom., cov: 31)
• Consequence: BNC2 NM_017637.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• Publications: 5 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BNC2	NM_017637.6	c.4-50953C>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.4-50953C>T		intron_variant	Intron 1 of 6	2	NM_017637.6	ENSP00000370047.3

Frequencies

GnomAD3 genomes AF: 0.842 AC: 127989 AN: 151960 Hom.: 54694 Cov.: 31

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.986

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.915

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.924

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.842 AC: 128068 AN: 152078 Hom.: 54721 Cov.: 31 AF XY: 0.842 AC XY: 62578 AN XY: 74312

African (AFR) AF: 0.687 AC: 28463 AN: 41438

American (AMR) AF: 0.853 AC: 13051 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.915 AC: 3176 AN: 3472

East Asian (EAS) AF: 0.746 AC: 3839 AN: 5146

South Asian (SAS) AF: 0.833 AC: 3989 AN: 4790

European-Finnish (FIN) AF: 0.918 AC: 9718 AN: 10586

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.924 AC: 62892 AN: 68034

Other (OTH) AF: 0.846 AC: 1788 AN: 2114

Alfa AF: 0.889 Hom.: 29646

Bravo AF: 0.826

Asia WGS AF: 0.787 AC: 2741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.9
DANN	Benign	0.81
PhyloP100		1.0
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: rs6475082; hg19: chr9-16789436;