rs1105282
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000517951.5(ADAM19):n.*1741+28140T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ADAM19
ENST00000517951.5 intron
ENST00000517951.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.658
Publications
18 publications found
Genes affected
ADAM19 (HGNC:197): (ADAM metallopeptidase domain 19) This gene encodes a member of the ADAM (a disintegrin and metalloprotease domain) family. Members of this family are membrane-anchored proteins 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. This member is a type I transmembrane protein and serves as a marker for dendritic cell differentiation. It has been demonstrated to be an active metalloproteinase, which may be involved in normal physiological processes such as cell migration, cell adhesion, cell-cell and cell-matrix interactions, and signal transduction. It is proposed to play a role in pathological processes, such as cancer, inflammatory diseases, renal diseases, and Alzheimer's disease. [provided by RefSeq, May 2013]
NIPAL4 (HGNC:28018): (NIPA like domain containing 4) This gene likely encodes a membrane receptor. Mutations in this gene have been associated with autosomal recessive congenital ichthyosis. [provided by RefSeq, Feb 2010]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| NIPAL4 | NM_001099287.2 | c.-196A>C | upstream_gene_variant | ENST00000311946.8 | NP_001092757.2 | |||
| NIPAL4 | NM_001172292.2 | c.-196A>C | upstream_gene_variant | NP_001165763.2 | ||||
| NIPAL4-DT | NR_136204.1 | n.-25T>G | upstream_gene_variant | |||||
| NIPAL4-DT | NR_136205.1 | n.-25T>G | upstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1259388Hom.: 0 Cov.: 28 AF XY: 0.00 AC XY: 0AN XY: 610074
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1259388
Hom.:
Cov.:
28
AF XY:
AC XY:
0
AN XY:
610074
African (AFR)
AF:
AC:
0
AN:
24194
American (AMR)
AF:
AC:
0
AN:
15858
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
17440
East Asian (EAS)
AF:
AC:
0
AN:
30418
South Asian (SAS)
AF:
AC:
0
AN:
59056
European-Finnish (FIN)
AF:
AC:
0
AN:
44118
Middle Eastern (MID)
AF:
AC:
0
AN:
3908
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1012788
Other (OTH)
AF:
AC:
0
AN:
51608
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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