chr15-83837802-G-GA
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_207517.3(ADAMTSL3):c.601-275dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 135,502 control chromosomes in the GnomAD database, including 1,803 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.15 ( 1803 hom., cov: 27)
Consequence
ADAMTSL3
NM_207517.3 intron
NM_207517.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.77
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 15-83837802-G-GA is Benign according to our data. Variant chr15-83837802-G-GA is described in ClinVar as [Benign]. Clinvar id is 1285835.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAMTSL3 | NM_207517.3 | c.601-275dup | intron_variant | ENST00000286744.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAMTSL3 | ENST00000286744.10 | c.601-275dup | intron_variant | 1 | NM_207517.3 | P1 | |||
ADAMTSL3 | ENST00000567476.1 | c.601-275dup | intron_variant | 1 | |||||
ADAMTSL3 | ENST00000561483.5 | n.816-275dup | intron_variant, non_coding_transcript_variant | 5 | |||||
ADAMTSL3 | ENST00000569510.5 | n.816-275dup | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.149 AC: 20144AN: 135464Hom.: 1807 Cov.: 27
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: 0.149 AC: 20133AN: 135502Hom.: 1803 Cov.: 27 AF XY: 0.147 AC XY: 9594AN XY: 65068
GnomAD4 genome
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65068
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 18, 2021 | - - |
Computational scores
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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