dbSNP rs3815501: BZW1:c.1228+94T>C (chr2-200821399-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001207067.2(BZW1):c.1228+94T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 1,473,268 control chromosomes in the GnomAD database, including 471,296 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 0.78 ( 46618 hom., cov: 32)

Exomes 𝑓: 0.80 ( 424678 hom. )

Consequence

BZW1
NM_001207067.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.393

Variant links:

Genes affected

BZW1 (HGNC:18380): (basic leucine zipper and W2 domains 1) Enables RNA binding activity and cadherin binding activity. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

BZW1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BZW1	NM_001207067.2 link	c.1228+94T>C		intron_variant	Intron 11 of 11	ENST00000409600.6	NP_001193996.1	Q7L1Q6-1Q3LIC9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
BZW1	ENST00000409600.6 link	c.1228+94T>C	intron_variant	Intron 11 of 11	1	NM_001207067.2	ENSP00000386474.1	Q7L1Q6-1
BZW1	ENST00000452790.6 link	c.1324+94T>C	intron_variant	Intron 11 of 11	2		ENSP00000394316.2	Q7L1Q6-3
BZW1	ENST00000409226.5 link	c.1240+94T>C	intron_variant	Intron 11 of 11	2		ENSP00000386837.1	Q7L1Q6-4
BZW1	ENST00000359893.4 link	c.373+94T>C	intron_variant	Intron 4 of 4	3		ENSP00000395673.1	H0Y503

Frequencies

GnomAD3 genomes

AF:

0.778

AC:

118309

AN:

152022

Hom.:

46593

Cov.:

show subpopulations

Gnomad AFR

AF:

0.780

Gnomad AMI

AF:

0.819

Gnomad AMR

AF:

0.686

Gnomad ASJ

AF:

0.798

Gnomad EAS

AF:

0.482

Gnomad SAS

AF:

0.589

Gnomad FIN

AF:

0.792

Gnomad MID

AF:

0.720

Gnomad NFE

AF:

0.830

Gnomad OTH

AF:

0.779

GnomAD4 exome

AF:

0.796

AC:

1052269

AN:

1321128

Hom.:

424678

AF XY:

0.792

AC XY:

518826

AN XY:

655294

show subpopulations

Gnomad4 AFR exome

AF:

0.773

Gnomad4 AMR exome

AF:

0.596

Gnomad4 ASJ exome

AF:

0.795

Gnomad4 EAS exome

AF:

0.446

Gnomad4 SAS exome

AF:

0.612

Gnomad4 FIN exome

AF:

0.800

Gnomad4 NFE exome

AF:

0.831

Gnomad4 OTH exome

AF:

0.778

GnomAD4 genome

AF:

0.778

AC:

118379

AN:

152140

Hom.:

46618

Cov.:

AF XY:

0.768

AC XY:

57143

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.780

Gnomad4 AMR

AF:

0.685

Gnomad4 ASJ

AF:

0.798

Gnomad4 EAS

AF:

0.482

Gnomad4 SAS

AF:

0.589

Gnomad4 FIN

AF:

0.792

Gnomad4 NFE

AF:

0.830

Gnomad4 OTH

AF:

0.778

Alfa

AF:

0.810

Hom.:

67931

Bravo

AF:

0.773

Asia WGS

AF:

0.546

AC:

1899

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

2.6

DANN

Benign

0.56

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over