rs10756819

Variant names:

• chr9-16858086-G-A
• rs10756819
• NM_017637.6:c.3+12560C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-16858086-G-A
• chr9-16858086-G-C
• chr9-16858086-G-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_017637.6(BNC2):​c.3+12560C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 152,050 control chromosomes in the GnomAD database, including 23,155 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 0.51 (23155 hom., cov: 33)
• Consequence: BNC2 NM_017637.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167
• Publications: 27 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BNC2	NM_017637.6	c.3+12560C>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.3+12560C>T		intron_variant	Intron 1 of 6	2	NM_017637.6	ENSP00000370047.3

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76904 AN: 151934 Hom.: 23150 Cov.: 33

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.506 AC: 76906 AN: 152050 Hom.: 23155 Cov.: 33 AF XY: 0.510 AC XY: 37927 AN XY: 74334

African (AFR) AF: 0.160 AC: 6644 AN: 41500

American (AMR) AF: 0.567 AC: 8656 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2139 AN: 3468

East Asian (EAS) AF: 0.542 AC: 2796 AN: 5162

South Asian (SAS) AF: 0.562 AC: 2706 AN: 4816

European-Finnish (FIN) AF: 0.680 AC: 7184 AN: 10566

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44936 AN: 67950

Other (OTH) AF: 0.536 AC: 1134 AN: 2114

Alfa AF: 0.610 Hom.: 91652

Bravo AF: 0.484

Asia WGS AF: 0.505 AC: 1758 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	15
DANN	Benign	0.69
PhyloP100		0.17
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: rs10756819; hg19: chr9-16858084;