chr8-24472122-CA-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -8 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAM7	NM_003817.4	c.633+3318delA		intron_variant	Intron 7 of 21	ENST00000175238.10	NP_003808.2
ADAM7-AS1	NR_125808.1	n.79+76417delT		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAM7	ENST00000175238.10	c.633+3303delA		intron_variant	Intron 7 of 21	1	NM_003817.4	ENSP00000175238.5
ADAM7	ENST00000380789.5	c.633+3303delA		intron_variant	Intron 7 of 22	5		ENSP00000370166.1
ADAM7-AS1	ENST00000519689.1	n.185-84132delT		intron_variant	Intron 2 of 4	4
ADAM7-AS1	ENST00000523578.5	n.79+76417delT		intron_variant	Intron 1 of 3	4

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

Gnomad4 AFR AF: 0.0423

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.0661

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.125

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs55708871; hg19: chr8-24329635;