rs1423300
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_030955.4(ADAMTS12):c.489+48791C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 152,012 control chromosomes in the GnomAD database, including 19,243 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 0.46 ( 19243 hom., cov: 32)
Consequence
ADAMTS12
NM_030955.4 intron
NM_030955.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.54
Genes affected
ADAMTS12 (HGNC:14605): (ADAM metallopeptidase with thrombospondin type 1 motif 12) This gene encodes a member of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) protein family. Members of the family share several distinct protein modules, including a propeptide region, a metalloproteinase domain, a disintegrin-like domain, and a thrombospondin type 1 (TS-1) motif. Individual members of this family differ in the number of C-terminal TS-1 motifs, and some have unique C-terminal domains. The enzyme encoded by this gene contains eight TS-1 motifs. It may play roles in pulmonary cells during fetal development or in tumor processes through its proteolytic activity or as a molecule potentially involved in regulation of cell adhesion. [provided by RefSeq, Jul 2008]
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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 (AFR) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAMTS12 | NM_030955.4 | c.489+48791C>T | intron_variant | ENST00000504830.6 | |||
ADAMTS12 | NM_001324511.2 | c.489+48791C>T | intron_variant | ||||
ADAMTS12 | NM_001324512.2 | c.489+48791C>T | intron_variant | ||||
ADAMTS12 | XM_017009905.2 | c.489+48791C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAMTS12 | ENST00000504830.6 | c.489+48791C>T | intron_variant | 1 | NM_030955.4 | P1 | |||
ADAMTS12 | ENST00000352040.7 | c.489+48791C>T | intron_variant | 1 | |||||
ADAMTS12 | ENST00000515401.1 | c.489+48791C>T | intron_variant | 1 | |||||
ADAMTS12 | ENST00000504582.5 | n.169+7816C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.455 AC: 69057AN: 151892Hom.: 19187 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.455 AC: 69175AN: 152012Hom.: 19243 Cov.: 32 AF XY: 0.460 AC XY: 34187AN XY: 74292
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1946
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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