8-24491643-G-A

Variant names:

• chr8-24491643-G-A
• rs7836430
• NM_003817.4:c.1357-260G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003817.4(ADAM7):​c.1357-260G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,782 control chromosomes in the GnomAD database, including 13,577 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.41 (13577 hom., cov: 31)
• Consequence: ADAM7 NM_003817.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• 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-AS2 (HGNC:56153): (ADAM7 antisense RNA 2)

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 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.1357-260G>A		intron	N/A	NP_003808.2	A0A384MTL6
	ADAM7-AS1	NR_125808.1		n.79+56897C>T		intron	N/A
	ADAM7-AS2	NR_125809.1		n.747+217C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADAM7	ENST00000175238.10	TSL:1 MANE Select	c.1357-260G>A		intron	N/A	ENSP00000175238.5	Q9H2U9-1
	ADAM7	ENST00000520720.1	TSL:1	c.673-260G>A		intron	N/A	ENSP00000430400.1	E5RK87
	ADAM7	ENST00000380789.5	TSL:5	c.1357-260G>A		intron	N/A	ENSP00000370166.1	C9JK28

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62098 AN: 151664 Hom.: 13563 Cov.: 31

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.0973

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.409 AC: 62136 AN: 151782 Hom.: 13577 Cov.: 31 AF XY: 0.401 AC XY: 29710 AN XY: 74182

African (AFR) AF: 0.532 AC: 21988 AN: 41366

American (AMR) AF: 0.340 AC: 5179 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1333 AN: 3466

East Asian (EAS) AF: 0.0967 AC: 498 AN: 5148

South Asian (SAS) AF: 0.231 AC: 1112 AN: 4804

European-Finnish (FIN) AF: 0.378 AC: 3974 AN: 10518

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.391 AC: 26586 AN: 67918

Other (OTH) AF: 0.414 AC: 874 AN: 2110

Alfa AF: 0.290 Hom.: 787

Bravo AF: 0.415

Asia WGS AF: 0.217 AC: 759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.36
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

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: rs7836430; hg19: chr8-24349156;