rs7860932

Variant names:

• chr9-16786900-G-A
• rs7860932
• NM_017637.6:c.4-48415C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-16786900-G-A
• chr9-16786900-G-C
• chr9-16786900-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.4-48415C>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
• Publications: 2 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: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017637.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BNC2	NM_017637.6	MANE Select	c.4-48415C>T		intron	N/A	NP_060107.3
	BNC2	NM_001317940.2		c.45+45344C>T		intron	N/A	NP_001304869.1
	BNC2	NM_001317939.2		c.4-58903C>T		intron	N/A	NP_001304868.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BNC2	ENST00000380672.9	TSL:2 MANE Select	c.4-48415C>T		intron	N/A	ENSP00000370047.3	Q6ZN30-1
	BNC2	ENST00000545497.5	TSL:1	c.-393-58903C>T		intron	N/A	ENSP00000444640.2	F5H586
	BNC2	ENST00000613349.4	TSL:1	c.-105-58903C>T		intron	N/A	ENSP00000477717.1	Q06HC7

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

African (AFR) AF: 0.852 AC: 35360 AN: 41482

American (AMR) AF: 0.882 AC: 13465 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.916 AC: 3182 AN: 3472

East Asian (EAS) AF: 0.792 AC: 4074 AN: 5144

South Asian (SAS) AF: 0.829 AC: 3991 AN: 4814

European-Finnish (FIN) AF: 0.903 AC: 9584 AN: 10618

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.911 AC: 61993 AN: 68032

Other (OTH) AF: 0.885 AC: 1872 AN: 2116

Alfa AF: 0.898 Hom.: 77139

Bravo AF: 0.881

Asia WGS AF: 0.795 AC: 2767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.3
DANN	Benign	0.56
PhyloP100		-0.50
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: rs7860932; hg19: chr9-16786898;