rs16838282

Variant names:

• chr2-206463871-A-G
• rs16838282
• NM_003812.4:c.433-17361A>G

Variant summary

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

The NM_003812.4(ADAM23):​c.433-17361A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.098 in 152,340 control chromosomes in the GnomAD database, including 918 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 0.098 (918 hom., cov: 33)
• Consequence: ADAM23 NM_003812.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120
• Publications: 4 publications found

Genes affected

ADAM23 (HGNC:202): (ADAM metallopeptidase domain 23) 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. It is reported that inactivation of this gene is associated with tumorigenesis in human cancers. [provided by RefSeq, May 2013]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003812.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAM23	NM_003812.4	MANE Select	c.433-17361A>G		intron	N/A	NP_003803.1
	ADAM23	NM_001410985.1		c.433-17361A>G		intron	N/A	NP_001397914.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAM23	ENST00000264377.8	TSL:1 MANE Select	c.433-17361A>G		intron	N/A	ENSP00000264377.3
	ADAM23	ENST00000374415.7	TSL:5	c.433-17361A>G		intron	N/A	ENSP00000363536.3

Frequencies

GnomAD3 genomes AF: 0.0980 AC: 14915 AN: 152222 Hom.: 913 Cov.: 33

Gnomad AFR AF: 0.0259

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0982

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.0980 AC: 14927 AN: 152340 Hom.: 918 Cov.: 33 AF XY: 0.0996 AC XY: 7416 AN XY: 74470

African (AFR) AF: 0.0258 AC: 1075 AN: 41590

American (AMR) AF: 0.0981 AC: 1501 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 557 AN: 3470

East Asian (EAS) AF: 0.146 AC: 756 AN: 5174

South Asian (SAS) AF: 0.114 AC: 550 AN: 4830

European-Finnish (FIN) AF: 0.137 AC: 1450 AN: 10616

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8626 AN: 68030

Other (OTH) AF: 0.119 AC: 252 AN: 2116

Alfa AF: 0.109 Hom.: 440

Bravo AF: 0.0924

Asia WGS AF: 0.126 AC: 437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.9
DANN	Benign	0.59
PhyloP100		0.12
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: rs16838282; hg19: chr2-207328595;