chr15-83819777-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_207517.3(ADAMTSL3):c.364-34T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 1,530,012 control chromosomes in the GnomAD database, including 25,597 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.14 ( 2001 hom., cov: 31)
Exomes 𝑓: 0.18 ( 23596 hom. )
Consequence
ADAMTSL3
NM_207517.3 intron
NM_207517.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.17
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 15-83819777-T-C is Benign according to our data. Variant chr15-83819777-T-C is described in ClinVar as [Benign]. Clinvar id is 1252346.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAMTSL3 | NM_207517.3 | c.364-34T>C | intron_variant | ENST00000286744.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAMTSL3 | ENST00000286744.10 | c.364-34T>C | intron_variant | 1 | NM_207517.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.142 AC: 21542AN: 151866Hom.: 2004 Cov.: 31
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GnomAD3 exomes AF: 0.163 AC: 40829AN: 250086Hom.: 3876 AF XY: 0.170 AC XY: 22961AN XY: 135192
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GnomAD4 exome AF: 0.177 AC: 244594AN: 1378038Hom.: 23596 Cov.: 23 AF XY: 0.179 AC XY: 123510AN XY: 689828
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GnomAD4 genome ? AF: 0.142 AC: 21540AN: 151974Hom.: 2001 Cov.: 31 AF XY: 0.141 AC XY: 10461AN XY: 74292
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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 | Nov 10, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at