1-150551891-CAAAAAAA-CAAAAAAAAAAA
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_019032.6(ADAMTSL4):c.-84-302_-84-299dupAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000108 in 92,750 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000011 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ADAMTSL4
NM_019032.6 intron
NM_019032.6 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.855
Publications
0 publications found
Genes affected
ADAMTSL4 (HGNC:19706): (ADAMTS like 4) This gene is a member of ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs)-like gene family and encodes a protein with seven thrombospondin type 1 repeats. The thrombospondin type 1 repeat domain is found in many proteins with diverse biological functions including cellular adhesion, angiogenesis, and patterning of the developing nervous system. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Sep 2014]
ADAMTSL4-AS2 (HGNC:40895): (ADAMTSL4 antisense RNA 2)
MIR4257 (HGNC:38312): (microRNA 4257) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_019032.6. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ADAMTSL4 | NM_019032.6 | MANE Select | c.-84-302_-84-299dupAAAA | intron | N/A | NP_061905.2 | |||
| ADAMTSL4 | NM_001288608.2 | c.-84-302_-84-299dupAAAA | intron | N/A | NP_001275537.1 | Q6UY14-3 | |||
| ADAMTSL4 | NM_001378596.1 | c.-84-302_-84-299dupAAAA | intron | N/A | NP_001365525.1 | Q6UY14-1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ADAMTSL4 | ENST00000271643.9 | TSL:5 MANE Select | c.-84-325_-84-324insAAAA | intron | N/A | ENSP00000271643.4 | Q6UY14-1 | ||
| ADAMTSL4 | ENST00000483335.1 | TSL:1 | n.1800_1801insAAAA | non_coding_transcript_exon | Exon 3 of 3 | ||||
| ADAMTSL4 | ENST00000369039.9 | TSL:5 | c.-84-325_-84-324insAAAA | intron | N/A | ENSP00000358035.5 | Q6UY14-3 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 92728Hom.: 0 Cov.: 30
GnomAD3 genomes
AF:
AC:
0
AN:
92728
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 25954Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 13350
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
25954
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
13350
African (AFR)
AF:
AC:
0
AN:
776
American (AMR)
AF:
AC:
0
AN:
1274
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
938
East Asian (EAS)
AF:
AC:
0
AN:
1526
South Asian (SAS)
AF:
AC:
0
AN:
1036
European-Finnish (FIN)
AF:
AC:
0
AN:
1290
Middle Eastern (MID)
AF:
AC:
0
AN:
476
European-Non Finnish (NFE)
AF:
AC:
0
AN:
16966
Other (OTH)
AF:
AC:
0
AN:
1672
GnomAD4 genome 0.0000108 AC: 1AN: 92750Hom.: 0 Cov.: 30 AF XY: 0.0000229 AC XY: 1AN XY: 43742 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
92750
Hom.:
Cov.:
30
AF XY:
AC XY:
1
AN XY:
43742
show subpopulations
African (AFR)
AF:
AC:
1
AN:
26468
American (AMR)
AF:
AC:
0
AN:
8604
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
2326
East Asian (EAS)
AF:
AC:
0
AN:
3292
South Asian (SAS)
AF:
AC:
0
AN:
3036
European-Finnish (FIN)
AF:
AC:
0
AN:
4762
Middle Eastern (MID)
AF:
AC:
0
AN:
168
European-Non Finnish (NFE)
AF:
AC:
0
AN:
42374
Other (OTH)
AF:
AC:
0
AN:
1198
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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