8-24472122-C-CA

Position:

• chr8-24472122-C-CA

Variant summary

Our verdict is Benign. Variant got -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

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 -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADAM7	NM_003817.4	c.633+3318dupA		intron_variant		ENST00000175238.10	NP_003808.2
ADAM7-AS1	NR_125808.1	n.79+76417dupT		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADAM7	ENST00000175238.10	c.633+3302_633+3303insA		intron_variant		1	NM_003817.4	ENSP00000175238.5
ADAM7	ENST00000380789.5	c.633+3302_633+3303insA		intron_variant		5		ENSP00000370166.1
ADAM7-AS1	ENST00000519689.1	n.185-84132_185-84131insT		intron_variant		4
ADAM7-AS1	ENST00000523578.5	n.79+76417_79+76418insT		intron_variant		4

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

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.0620

Gnomad4 ASJ AF: 0.0598

Gnomad4 EAS AF: 0.110

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.00738

Gnomad4 NFE AF: 0.0298

Gnomad4 OTH AF: 0.108

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

case-control

Suna and Inan Kirac Foundation Neurodegeneration Research Laboratory, Koc University

Apr 02, 2020

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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;