rs6961256

Variant names:

• chr7-16691567-A-G
• rs6961256
• NM_014038.3:c.651+1661A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014038.3(BZW2):​c.651+1661A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0898 in 152,196 control chromosomes in the GnomAD database, including 1,689 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 0.090 (1689 hom., cov: 33)
• Consequence: BZW2 NM_014038.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436
• Publications: 1 publications found

Genes affected

BZW2 (HGNC:18808): (basic leucine zipper and W2 domains 2) Enables cadherin binding activity. Predicted to be involved in cell differentiation and nervous system development. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000235837 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014038.3. 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
	BZW2	NM_014038.3	MANE Select	c.651+1661A>G		intron	N/A	NP_054757.1	Q9Y6E2-1
	BZW2	NM_001159767.2		c.651+1661A>G		intron	N/A	NP_001153239.1	Q9Y6E2-1
	BZW2	NM_001362717.2		c.651+1661A>G		intron	N/A	NP_001349646.1	Q9Y6E2-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BZW2	ENST00000258761.8	TSL:1 MANE Select	c.651+1661A>G		intron	N/A	ENSP00000258761.3	Q9Y6E2-1
	BZW2	ENST00000415365.5	TSL:1	c.651+1661A>G		intron	N/A	ENSP00000403481.1	E7ETZ4
	BZW2	ENST00000437745.5	TSL:1	n.*29+1661A>G		intron	N/A	ENSP00000406395.1	E9PFE3

Frequencies

GnomAD3 genomes AF: 0.0898 AC: 13656 AN: 152078 Hom.: 1684 Cov.: 33

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0371

Gnomad ASJ AF: 0.00836

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0384

Gnomad FIN AF: 0.00913

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0139

Gnomad OTH AF: 0.0669

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

GnomAD4 genome AF: 0.0898 AC: 13670 AN: 152196 Hom.: 1689 Cov.: 33 AF XY: 0.0869 AC XY: 6469 AN XY: 74410

African (AFR) AF: 0.282 AC: 11699 AN: 41476

American (AMR) AF: 0.0370 AC: 566 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00836 AC: 29 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.0372 AC: 179 AN: 4814

European-Finnish (FIN) AF: 0.00913 AC: 97 AN: 10624

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0139 AC: 943 AN: 68020

Other (OTH) AF: 0.0658 AC: 139 AN: 2114

Alfa AF: 0.0470 Hom.: 258

Bravo AF: 0.101

Asia WGS AF: 0.0290 AC: 101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.52
PhyloP100		-0.44
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: rs6961256; hg19: chr7-16731192;