rs2853211

Variant names:

• chr20-3680300-G-C
• rs2853211
• NM_025220.5:c.98-729C>G

Variant summary

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

The NM_025220.5(ADAM33):​c.98-729C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 151,932 control chromosomes in the GnomAD database, including 3,154 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 0.20 (3154 hom., cov: 31)
• Consequence: ADAM33 NM_025220.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850
• Publications: 4 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAM33	NM_025220.5	c.98-729C>G		intron_variant	Intron 1 of 21	ENST00000356518.7	NP_079496.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAM33	ENST00000356518.7	c.98-729C>G		intron_variant	Intron 1 of 21	1	NM_025220.5	ENSP00000348912.3
ADAM33	ENST00000379861.8	c.98-729C>G		intron_variant	Intron 1 of 21	1		ENSP00000369190.4
ADAM33	ENST00000350009.6	c.98-729C>G		intron_variant	Intron 1 of 20	5		ENSP00000322550.5

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30320 AN: 151814 Hom.: 3154 Cov.: 31

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.235

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.200 AC: 30328 AN: 151932 Hom.: 3154 Cov.: 31 AF XY: 0.198 AC XY: 14673 AN XY: 74262

African (AFR) AF: 0.146 AC: 6052 AN: 41414

American (AMR) AF: 0.217 AC: 3313 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3470

East Asian (EAS) AF: 0.144 AC: 739 AN: 5142

South Asian (SAS) AF: 0.237 AC: 1140 AN: 4816

European-Finnish (FIN) AF: 0.201 AC: 2125 AN: 10584

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15436 AN: 67924

Other (OTH) AF: 0.233 AC: 491 AN: 2104

Alfa AF: 0.222 Hom.: 467

Bravo AF: 0.200

Asia WGS AF: 0.185 AC: 644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.9
DANN	Benign	0.72
PhyloP100		-0.085
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: rs2853211; hg19: chr20-3660947;