rs1029015

Variant names:

• chr9-16657398-A-C
• rs1029015
• NM_017637.6:c.330+70399T>G

Your query was ambiguous. Multiple possible variants found:

• chr9-16657398-A-C
• chr9-16657398-A-G
• chr9-16657398-A-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.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
• Publications: 4 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BNC2	NM_017637.6	MANE Select	c.330+70399T>G		intron	N/A	NP_060107.3
	BNC2	NM_001317940.2		c.46-74313T>G		intron	N/A	NP_001304869.1
	BNC2	NM_001317939.2		c.204+70399T>G		intron	N/A	NP_001304868.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BNC2	ENST00000380672.9	TSL:2 MANE Select	c.330+70399T>G		intron	N/A	ENSP00000370047.3
	BNC2	ENST00000545497.5	TSL:1	c.-193+70399T>G		intron	N/A	ENSP00000444640.2
	BNC2	ENST00000603713.5	TSL:1	c.96+70399T>G		intron	N/A	ENSP00000474045.1

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

African (AFR) AF: 0.208 AC: 8648 AN: 41518

American (AMR) AF: 0.592 AC: 9048 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1757 AN: 3466

East Asian (EAS) AF: 0.688 AC: 3551 AN: 5162

South Asian (SAS) AF: 0.378 AC: 1822 AN: 4818

European-Finnish (FIN) AF: 0.518 AC: 5472 AN: 10562

Middle Eastern (MID) AF: 0.634 AC: 185 AN: 292

European-Non Finnish (NFE) AF: 0.561 AC: 38151 AN: 67972

Other (OTH) AF: 0.525 AC: 1106 AN: 2108

Alfa AF: 0.498 Hom.: 2673

Bravo AF: 0.463

Asia WGS AF: 0.500 AC: 1741 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.0060
DANN	Benign	0.53
PhyloP100		-2.3
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: rs1029015; hg19: chr9-16657396;