chr8-24472122-CAAA-C

Variant names:

• chr8-24472122-CAAA-C
• rs55708871
• NM_003817.4:c.633+3316_633+3318delAAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_003817.4(ADAM7):​c.633+3316_633+3318delAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.029 in 102,754 control chromosomes in the GnomAD database, including 98 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.029 (98 hom., cov: 23)
• Consequence: ADAM7 NM_003817.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.682

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 (AFR) allele frequency at 95% confidence interval = 0.0903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADAM7	NM_003817.4	c.633+3316_633+3318delAAA		intron_variant	Intron 7 of 21	ENST00000175238.10	NP_003808.2
ADAM7-AS1	NR_125808.1	n.79+76415_79+76417delTTT		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADAM7	ENST00000175238.10	c.633+3303_633+3305delAAA		intron_variant	Intron 7 of 21	1	NM_003817.4	ENSP00000175238.5
ADAM7	ENST00000380789.5	c.633+3303_633+3305delAAA		intron_variant	Intron 7 of 22	5		ENSP00000370166.1
ADAM7-AS1	ENST00000519689.1	n.185-84134_185-84132delTTT		intron_variant	Intron 2 of 4	4
ADAM7-AS1	ENST00000523578.5	n.79+76415_79+76417delTTT		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.0290 AC: 2979 AN: 102762 Hom.: 98 Cov.: 23

Gnomad AFR AF: 0.0933

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0101

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00104

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000280

Gnomad OTH AF: 0.0180

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

GnomAD4 genome AF: 0.0290 AC: 2977 AN: 102754 Hom.: 98 Cov.: 23 AF XY: 0.0286 AC XY: 1404 AN XY: 49010

Gnomad4 AFR AF: 0.0932

Gnomad4 AMR AF: 0.0101

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000700

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000280

Gnomad4 OTH AF: 0.0179

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;