Variant rs2271511 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_025220.5(ADAM33):c.864G>A(p.Gly288=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 1,532,452 control chromosomes in the GnomAD database, including 30,692 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 0.24 ( 5049 hom., cov: 33)

Exomes 𝑓: 0.19 ( 25643 hom. )

Consequence

ADAM33
NM_025220.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.38

Variant links:

Genes affected

ADAM33 (HGNC:15478): (ADAM metallopeptidase domain 33) This gene encodes a member of the ADAM (a disintegrin and metalloprotease domain) family. Members of this family are membrane-anchored proteins structurally related to snake venom disintegrins, and have been implicated in a variety of biological processes involving cell-cell and cell-matrix interactions, including fertilization, muscle development, and neurogenesis. This protein is a type I transmembrane protein implicated in asthma and bronchial hyperresponsiveness. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Sep 2013]

ADAM33 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.72).

BP7

Synonymous conserved (PhyloP=-1.38 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADAM33	NM_025220.5 linkuse as main transcript	c.864G>A	p.Gly288=	synonymous_variant	9/22	ENST00000356518.7	NP_079496.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADAM33	ENST00000356518.7 linkuse as main transcript	c.864G>A	p.Gly288=	synonymous_variant	9/22	1	NM_025220.5	ENSP00000348912	P4	Q9BZ11-1
ADAM33	ENST00000379861.8 linkuse as main transcript	c.864G>A	p.Gly288=	synonymous_variant	9/22	1		ENSP00000369190	A2
ADAM33	ENST00000350009.6 linkuse as main transcript	c.864G>A	p.Gly288=	synonymous_variant	9/21	5		ENSP00000322550	A2	Q9BZ11-2
ADAM33	ENST00000466620.5 linkuse as main transcript			upstream_gene_variant		1

Frequencies

GnomAD3 genomes

AF:

0.242

AC:

36816

AN:

151998

Hom.:

5045

Cov.:

show subpopulations

Gnomad AFR

AF:

0.383

Gnomad AMI

AF:

0.141

Gnomad AMR

AF:

0.175

Gnomad ASJ

AF:

0.208

Gnomad EAS

AF:

0.195

Gnomad SAS

AF:

0.283

Gnomad FIN

AF:

0.204

Gnomad MID

AF:

0.283

Gnomad NFE

AF:

0.181

Gnomad OTH

AF:

0.250

GnomAD3 exomes

AF:

0.204

AC:

26659

AN:

130940

Hom.:

3093

AF XY:

0.210

AC XY:

15080

AN XY:

71872

show subpopulations

Gnomad AFR exome

AF:

0.391

Gnomad AMR exome

AF:

0.119

Gnomad ASJ exome

AF:

0.225

Gnomad EAS exome

AF:

0.196

Gnomad SAS exome

AF:

0.281

Gnomad FIN exome

AF:

0.199

Gnomad NFE exome

AF:

0.182

Gnomad OTH exome

AF:

0.208

GnomAD4 exome

AF:

0.188

AC:

258912

AN:

1380340

Hom.:

25643

Cov.:

AF XY:

0.191

AC XY:

129862

AN XY:

680838

show subpopulations

Gnomad4 AFR exome

AF:

0.387

Gnomad4 AMR exome

AF:

0.126

Gnomad4 ASJ exome

AF:

0.220

Gnomad4 EAS exome

AF:

0.196

Gnomad4 SAS exome

AF:

0.279

Gnomad4 FIN exome

AF:

0.212

Gnomad4 NFE exome

AF:

0.174

Gnomad4 OTH exome

AF:

0.205

GnomAD4 genome

AF:

0.242

AC:

36845

AN:

152112

Hom.:

5049

Cov.:

AF XY:

0.242

AC XY:

18026

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.383

Gnomad4 AMR

AF:

0.174

Gnomad4 ASJ

AF:

0.208

Gnomad4 EAS

AF:

0.196

Gnomad4 SAS

AF:

0.282

Gnomad4 FIN

AF:

0.204

Gnomad4 NFE

AF:

0.181

Gnomad4 OTH

AF:

0.249

Alfa

AF:

0.219

Hom.:

733

Bravo

AF:

0.241

Asia WGS

AF:

0.233

AC:

808

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.72

CADD

Benign

4.5

DANN

Benign

0.96

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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