rs10738445

Variant names:

• chr9-16680140-A-C
• rs10738445
• NM_017637.6:c.330+47657T>G

Your query was ambiguous. Multiple possible variants found:

• chr9-16680140-A-C
• chr9-16680140-A-G
• chr9-16680140-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+47657T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 152,040 control chromosomes in the GnomAD database, including 33,052 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 0.62 (33052 hom., cov: 33)
• Consequence: BNC2 NM_017637.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.959
• Publications: 13 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.802 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.330+47657T>G		intron	N/A	NP_060107.3
	BNC2	NM_001317940.2		c.46-97055T>G		intron	N/A	NP_001304869.1
	BNC2	NM_001317939.2		c.204+47657T>G		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.330+47657T>G		intron	N/A	ENSP00000370047.3	Q6ZN30-1
	BNC2	ENST00000545497.5	TSL:1	c.-193+47657T>G		intron	N/A	ENSP00000444640.2	F5H586
	BNC2	ENST00000603713.5	TSL:1	c.96+47657T>G		intron	N/A	ENSP00000474045.1	Q06HB9

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94838 AN: 151922 Hom.: 33050 Cov.: 33

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.783

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.624 AC: 94854 AN: 152040 Hom.: 33052 Cov.: 33 AF XY: 0.615 AC XY: 45734 AN XY: 74328

African (AFR) AF: 0.340 AC: 14111 AN: 41456

American (AMR) AF: 0.613 AC: 9353 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2449 AN: 3464

East Asian (EAS) AF: 0.380 AC: 1960 AN: 5160

South Asian (SAS) AF: 0.326 AC: 1571 AN: 4814

European-Finnish (FIN) AF: 0.783 AC: 8286 AN: 10580

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.808 AC: 54900 AN: 67982

Other (OTH) AF: 0.644 AC: 1363 AN: 2116

Alfa AF: 0.749 Hom.: 67308

Bravo AF: 0.608

Asia WGS AF: 0.327 AC: 1140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.4
DANN	Benign	0.57
PhyloP100		0.96
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: rs10738445; hg19: chr9-16680138;