rs6597731
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001288973.2(ADAM12):c.2530-1541G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 152,106 control chromosomes in the GnomAD database, including 31,043 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 0.63 ( 31043 hom., cov: 33)
Consequence
ADAM12
NM_001288973.2 intron
NM_001288973.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.34
Genes affected
ADAM12 (HGNC:190): (ADAM metallopeptidase domain 12) This gene encodes a member of a family of proteins that are structurally related to snake venom disintegrins and have been implicated in a variety of biological processes involving cell-cell and cell-matrix interactions, including fertilization, muscle development, and neurogenesis. Expression of this gene has been used as a maternal serum marker for pre-natal development. Alternative splicing results in multiple transcript variants encoding different isoforms. Shorter isoforms are secreted, while longer isoforms are membrane-bound form. [provided by RefSeq, Jan 2014]
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAM12 | NM_001288973.2 | c.2530-1541G>T | intron_variant | ENST00000448723.2 | |||
ADAM12 | NM_003474.6 | c.2539-1541G>T | intron_variant | ||||
ADAM12 | XM_017016706.2 | c.1372-1541G>T | intron_variant | ||||
ADAM12 | XM_024448210.1 | c.1201-1541G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAM12 | ENST00000448723.2 | c.2530-1541G>T | intron_variant | 5 | NM_001288973.2 | A2 | |||
ADAM12 | ENST00000368679.8 | c.2539-1541G>T | intron_variant | 1 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.632 AC: 96017AN: 151990Hom.: 31017 Cov.: 33
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: 0.632 AC: 96093AN: 152106Hom.: 31043 Cov.: 33 AF XY: 0.631 AC XY: 46905AN XY: 74362
GnomAD4 genome
?
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33
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46905
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74362
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2516
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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