rs4775085
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001110.4(ADAM10):c.585+7305C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.03 in 151,972 control chromosomes in the GnomAD database, including 95 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 0.030 ( 95 hom., cov: 32)
Consequence
ADAM10
NM_001110.4 intron
NM_001110.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.847
Genes affected
ADAM10 (HGNC:188): (ADAM metallopeptidase domain 10) Members of the ADAM family are cell surface proteins with a unique structure possessing both potential adhesion and protease domains. This gene encodes and ADAM family member that cleaves many proteins including TNF-alpha and E-cadherin. Alternate splicing results in multiple transcript variants encoding different proteins that may undergo similar processing. [provided by RefSeq, Feb 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.03 (4555/151972) while in subpopulation NFE AF= 0.0483 (3281/67982). AF 95% confidence interval is 0.0469. There are 95 homozygotes in gnomad4. There are 2129 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High AC in GnomAd at 4558 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAM10 | NM_001110.4 | c.585+7305C>T | intron_variant | ENST00000260408.8 | |||
ADAM10 | NM_001320570.2 | c.585+7305C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAM10 | ENST00000260408.8 | c.585+7305C>T | intron_variant | 1 | NM_001110.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0300 AC: 4558AN: 151862Hom.: 94 Cov.: 32
GnomAD3 genomes
?
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0300 AC: 4555AN: 151972Hom.: 95 Cov.: 32 AF XY: 0.0287 AC XY: 2129AN XY: 74270
GnomAD4 genome
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2129
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at