rs58370486

Positions:

• chr7-16668236-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_014038.3(BZW2):​c.58+2735A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,144 control chromosomes in the GnomAD database, including 1,970 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 0.10 (1970 hom., cov: 32)
• Consequence: BZW2 NM_014038.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BZW2	NM_014038.3	c.58+2735A>G		intron_variant		ENST00000258761.8	NP_054757.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BZW2	ENST00000258761.8	c.58+2735A>G		intron_variant		1	NM_014038.3	ENSP00000258761	P1

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15795 AN: 152026 Hom.: 1966 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.0584

Gnomad ASJ AF: 0.0602

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00890

Gnomad FIN AF: 0.00858

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0261

Gnomad OTH AF: 0.0831

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

GnomAD4 genome AF: 0.104 AC: 15814 AN: 152144 Hom.: 1970 Cov.: 32 AF XY: 0.100 AC XY: 7439 AN XY: 74410

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.0582

Gnomad4 ASJ AF: 0.0602

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00870

Gnomad4 FIN AF: 0.00858

Gnomad4 NFE AF: 0.0261

Gnomad4 OTH AF: 0.0822

Alfa AF: 0.0766 Hom.: 334

Bravo AF: 0.118

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	5.7
DANN	Benign	0.77

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

Publications

LitVar

Other links and lift over

dbSNP: rs58370486; hg19: chr7-16707861;