7-16661173-G-A

Variant names:

• chr7-16661173-G-A
• rs696279
• NM_014038.3:c.-7-4264G>A

Variant summary

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

The NM_014038.3(BZW2):​c.-7-4264G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.583 in 151,932 control chromosomes in the GnomAD database, including 26,648 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 0.58 (26648 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: BZW2 NM_014038.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173
• Publications: 11 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BZW2	NM_014038.3	c.-7-4264G>A		intron_variant	Intron 1 of 11	ENST00000258761.8	NP_054757.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BZW2	ENST00000258761.8	c.-7-4264G>A		intron_variant	Intron 1 of 11	1	NM_014038.3	ENSP00000258761.3

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88548 AN: 151810 Hom.: 26617 Cov.: 32

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.563

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.583 AC: 88628 AN: 151930 Hom.: 26648 Cov.: 32 AF XY: 0.577 AC XY: 42844 AN XY: 74228

African (AFR) AF: 0.716 AC: 29699 AN: 41484

American (AMR) AF: 0.558 AC: 8514 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1553 AN: 3468

East Asian (EAS) AF: 0.407 AC: 2103 AN: 5168

South Asian (SAS) AF: 0.502 AC: 2422 AN: 4820

European-Finnish (FIN) AF: 0.531 AC: 5600 AN: 10544

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 36982 AN: 67862

Other (OTH) AF: 0.563 AC: 1188 AN: 2110

Alfa AF: 0.551 Hom.: 97471

Bravo AF: 0.589

Asia WGS AF: 0.448 AC: 1555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.23
DANN	Benign	0.44
PhyloP100		-0.17
PromoterAI		-0.067	Neutral
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: rs696279; hg19: chr7-16700798;