8-24472122-CAAAAAAAA-CAAAAAAA

Variant names:

• chr8-24472122-CA-C
• rs55708871
• NM_003817.4:c.633+3318delA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_003817.4(ADAM7):​c.633+3318delA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 102,684 control chromosomes in the GnomAD database, including 609 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.12 (609 hom., cov: 23)
• Consequence: ADAM7 NM_003817.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.386
• Publications: 0 publications found

Genes affected

ADAM7 (HGNC:214): (ADAM metallopeptidase domain 7) This gene encodes a member of the ADAMs family of zinc proteases. These transmembrane proteins play roles in multiple processes including cell signaling, adhesion and migration. The encoded protein lacks protease activity and may play roles in protein-protein interactions and cell adhesion processes including sperm-egg fusion. Mutations in this gene may be involved in the progression of melanoma. [provided by RefSeq, Oct 2011]

ADAM7-AS1 (HGNC:56152): (ADAM7, ADAMDEC1 and ADAM28 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003817.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAM7	NM_003817.4	MANE Select	c.633+3318delA		intron	N/A	NP_003808.2	A0A384MTL6
	ADAM7-AS1	NR_125808.1		n.79+76417delT		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAM7	ENST00000175238.10	TSL:1 MANE Select	c.633+3303delA		intron	N/A	ENSP00000175238.5	Q9H2U9-1
	ADAM7	ENST00000380789.5	TSL:5	c.633+3303delA		intron	N/A	ENSP00000370166.1	C9JK28
	ADAM7-AS1	ENST00000519689.1	TSL:4	n.185-84132delT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.122 AC: 12495 AN: 102692 Hom.: 608 Cov.: 23

Gnomad AFR AF: 0.0423

Gnomad AMI AF: 0.0927

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.0665

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.122 AC: 12487 AN: 102684 Hom.: 609 Cov.: 23 AF XY: 0.117 AC XY: 5742 AN XY: 48990

African (AFR) AF: 0.0423 AC: 1291 AN: 30502

American (AMR) AF: 0.102 AC: 965 AN: 9422

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 374 AN: 2452

East Asian (EAS) AF: 0.187 AC: 694 AN: 3710

South Asian (SAS) AF: 0.0661 AC: 189 AN: 2858

European-Finnish (FIN) AF: 0.106 AC: 544 AN: 5144

Middle Eastern (MID) AF: 0.124 AC: 22 AN: 178

European-Non Finnish (NFE) AF: 0.176 AC: 8171 AN: 46364

Other (OTH) AF: 0.125 AC: 181 AN: 1450

Alfa AF: 0.0222 Hom.: 13

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.39

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: rs55708871; hg19: chr8-24329635;