Variant 20-3671095-C-G 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.2151G>C(p.Gly717Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 1,593,178 control chromosomes in the GnomAD database, including 74,095 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 0.38 ( 12821 hom., cov: 34)

Exomes 𝑓: 0.28 ( 61274 hom. )

Consequence

ADAM33
NM_025220.5 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.476

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:

ADAM33 (HGNC:):

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=-0.71).

BP7

Synonymous conserved (PhyloP=0.476 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.629 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.2151G>C	p.Gly717Gly	synonymous_variant	19/22	ENST00000356518.7	NP_079496.1	Q9BZ11-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
ADAM33	ENST00000356518.7 linkuse as main transcript	c.2151G>C	p.Gly717Gly	synonymous_variant	19/22	1	NM_025220.5	ENSP00000348912.3	Q9BZ11-1
ADAM33	ENST00000379861.8 linkuse as main transcript	c.2151G>C	p.Gly717Gly	synonymous_variant	19/22	1		ENSP00000369190.4	A2A2L3
ADAM33	ENST00000466620.5 linkuse as main transcript	n.1712G>C		non_coding_transcript_exon_variant	8/11	1
ADAM33	ENST00000350009.6 linkuse as main transcript	c.2073G>C	p.Gly691Gly	synonymous_variant	18/21	5		ENSP00000322550.5	Q9BZ11-2

Frequencies

GnomAD3 genomes

AF:

0.379

AC:

57615

AN:

152016

Hom.:

12804

Cov.:

show subpopulations

Gnomad AFR

AF:

0.635

Gnomad AMI

AF:

0.220

Gnomad AMR

AF:

0.257

Gnomad ASJ

AF:

0.271

Gnomad EAS

AF:

0.231

Gnomad SAS

AF:

0.349

Gnomad FIN

AF:

0.355

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.276

Gnomad OTH

AF:

0.359

GnomAD3 exomes

AF:

0.294

AC:

63195

AN:

214728

Hom.:

10528

AF XY:

0.297

AC XY:

34500

AN XY:

116198

show subpopulations

Gnomad AFR exome

AF:

0.646

Gnomad AMR exome

AF:

0.158

Gnomad ASJ exome

AF:

0.286

Gnomad EAS exome

AF:

0.226

Gnomad SAS exome

AF:

0.363

Gnomad FIN exome

AF:

0.346

Gnomad NFE exome

AF:

0.272

Gnomad OTH exome

AF:

0.287

GnomAD4 exome

AF:

0.283

AC:

407690

AN:

1441044

Hom.:

61274

Cov.:

AF XY:

0.285

AC XY:

203946

AN XY:

715108

show subpopulations

Gnomad4 AFR exome

AF:

0.649

Gnomad4 AMR exome

AF:

0.167

Gnomad4 ASJ exome

AF:

0.285

Gnomad4 EAS exome

AF:

0.237

Gnomad4 SAS exome

AF:

0.362

Gnomad4 FIN exome

AF:

0.352

Gnomad4 NFE exome

AF:

0.267

Gnomad4 OTH exome

AF:

0.302

GnomAD4 genome

AF:

0.379

AC:

57672

AN:

152134

Hom.:

12821

Cov.:

AF XY:

0.380

AC XY:

28266

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.635

Gnomad4 AMR

AF:

0.256

Gnomad4 ASJ

AF:

0.271

Gnomad4 EAS

AF:

0.231

Gnomad4 SAS

AF:

0.348

Gnomad4 FIN

AF:

0.355

Gnomad4 NFE

AF:

0.276

Gnomad4 OTH

AF:

0.357

Alfa

AF:

0.227

Hom.:

777

Bravo

AF:

0.376

Asia WGS

AF:

0.289

AC:

1004

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

DANN

Benign

0.64

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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