8-24493099-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_003817.4(ADAM7):ā€‹c.1712G>Cā€‹(p.Gly571Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,459,832 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 6.9e-7 ( 0 hom. )

Consequence

ADAM7
NM_003817.4 missense

Scores

5
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.70
Variant links:
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)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.33614996).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ADAM7NM_003817.4 linkc.1712G>C p.Gly571Ala missense_variant 16/22 ENST00000175238.10 NP_003808.2 Q9H2U9-1A0A384MTL6
ADAM7-AS1NR_125808.1 linkn.79+55441C>G intron_variant
ADAM7-AS2NR_125809.1 linkn.447-939C>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ADAM7ENST00000175238.10 linkc.1712G>C p.Gly571Ala missense_variant 16/221 NM_003817.4 ENSP00000175238.5 Q9H2U9-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.85e-7
AC:
1
AN:
1459832
Hom.:
0
Cov.:
30
AF XY:
0.00000138
AC XY:
1
AN XY:
726256
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.00e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJun 05, 2024The c.1712G>C (p.G571A) alteration is located in exon 16 (coding exon 16) of the ADAM7 gene. This alteration results from a G to C substitution at nucleotide position 1712, causing the glycine (G) at amino acid position 571 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.17
BayesDel_addAF
Benign
-0.24
T
BayesDel_noAF
Benign
-0.58
CADD
Benign
23
DANN
Uncertain
0.99
DEOGEN2
Benign
0.013
T;T;.
Eigen
Uncertain
0.31
Eigen_PC
Benign
0.16
FATHMM_MKL
Uncertain
0.88
D
LIST_S2
Benign
0.79
T;T;T
M_CAP
Benign
0.018
T
MetaRNN
Benign
0.34
T;T;T
MetaSVM
Benign
-0.87
T
MutationAssessor
Uncertain
2.8
M;.;.
PrimateAI
Benign
0.36
T
PROVEAN
Uncertain
-2.6
D;D;D
REVEL
Benign
0.25
Sift
Benign
0.045
D;D;T
Sift4G
Benign
0.070
T;D;D
Polyphen
1.0
D;.;D
Vest4
0.16
MutPred
0.58
Loss of disorder (P = 0.0973);Loss of disorder (P = 0.0973);.;
MVP
0.45
MPC
0.31
ClinPred
0.98
D
GERP RS
4.8
Varity_R
0.21
gMVP
0.70

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.12
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1239880009; hg19: chr8-24350612; API