chr8-24472122-C-CA

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_003817.4(ADAM7):​c.633+3318dupA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 102,608 control chromosomes in the GnomAD database, including 1,002 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.11 (1002 hom., cov: 23)
• Consequence: ADAM7 NM_003817.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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 -10 ACMG points.

• BP6: Variant 8-24472122-C-CA is Benign according to our data. Variant chr8-24472122-C-CA is described in ClinVar as Benign. ClinVar VariationId is 873299.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 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+3318dupA		intron	N/A	NP_003808.2	A0A384MTL6
	ADAM7-AS1	NR_125808.1		n.79+76417dupT		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+3302_633+3303insA		intron	N/A	ENSP00000175238.5	Q9H2U9-1
	ADAM7	ENST00000380789.5	TSL:5	c.633+3302_633+3303insA		intron	N/A	ENSP00000370166.1	C9JK28
	ADAM7-AS1	ENST00000519689.1	TSL:4	n.185-84132_185-84131insT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.112 AC: 11494 AN: 102616 Hom.: 1002 Cov.: 23

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.0497

Gnomad AMR AF: 0.0620

Gnomad ASJ AF: 0.0598

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.00738

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0298

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.112 AC: 11495 AN: 102608 Hom.: 1002 Cov.: 23 AF XY: 0.111 AC XY: 5416 AN XY: 48942

African (AFR) AF: 0.277 AC: 8422 AN: 30418

American (AMR) AF: 0.0620 AC: 584 AN: 9424

Ashkenazi Jewish (ASJ) AF: 0.0598 AC: 147 AN: 2458

East Asian (EAS) AF: 0.110 AC: 408 AN: 3706

South Asian (SAS) AF: 0.107 AC: 305 AN: 2856

European-Finnish (FIN) AF: 0.00738 AC: 38 AN: 5146

Middle Eastern (MID) AF: 0.112 AC: 20 AN: 178

European-Non Finnish (NFE) AF: 0.0298 AC: 1384 AN: 46368

Other (OTH) AF: 0.108 AC: 157 AN: 1450

Alfa AF: 0.00460 Hom.: 13

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

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;