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

Variant summary

Our verdict is Benign. The variant received -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

Publications

12 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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

African (AFR)

AF:

0.773

AC:

23070

AN:

29830

American (AMR)

AF:

0.596

AC:

20569

AN:

34528

Ashkenazi Jewish (ASJ)

AF:

0.795

AC:

17614

AN:

22154

East Asian (EAS)

AF:

0.446

AC:

16985

AN:

38088

South Asian (SAS)

AF:

0.612

AC:

44131

AN:

72150

European-Finnish (FIN)

AF:

0.800

AC:

30882

AN:

38624

Middle Eastern (MID)

AF:

0.765

AC:

3939

AN:

5148

European-Non Finnish (NFE)

AF:

0.831

AC:

852197

AN:

1025464

Other (OTH)

AF:

0.778

AC:

42882

AN:

55142

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

9239

18478

27716

36955

46194

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19452

38904

58356

77808

97260

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.778

AC:

118379

AN:

152140

Hom.:

46618

Cov.:

AF XY:

0.768

AC XY:

57143

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.780

AC:

32371

AN:

41492

American (AMR)

AF:

0.685

AC:

10482

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.798

AC:

2765

AN:

3466

East Asian (EAS)

AF:

0.482

AC:

2493

AN:

5176

South Asian (SAS)

AF:

0.589

AC:

2836

AN:

4812

European-Finnish (FIN)

AF:

0.792

AC:

8369

AN:

10570

Middle Eastern (MID)

AF:

0.729

AC:

213

AN:

292

European-Non Finnish (NFE)

AF:

0.830

AC:

56466

AN:

68016

Other (OTH)

AF:

0.778

AC:

1639

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1313

2626

3940

5253

6566

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

856

1712

2568

3424

4280

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.806

Hom.:

104021

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

(source)

DANN

Benign

0.56

PhyloP100

-0.39

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over