rs2401171
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_207517.3(ADAMTSL3):c.1073-1185T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 152,088 control chromosomes in the GnomAD database, including 30,955 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 0.62 ( 30955 hom., cov: 32)
Consequence
ADAMTSL3
NM_207517.3 intron
NM_207517.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.620
Genes affected
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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=-0.83).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADAMTSL3 | NM_207517.3 | c.1073-1185T>G | intron_variant | ENST00000286744.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADAMTSL3 | ENST00000286744.10 | c.1073-1185T>G | intron_variant | 1 | NM_207517.3 | P1 | |||
ADAMTSL3 | ENST00000567476.1 | c.1073-1185T>G | intron_variant | 1 | |||||
ADAMTSL3 | ENST00000561483.5 | n.1288-1185T>G | intron_variant, non_coding_transcript_variant | 5 | |||||
ADAMTSL3 | ENST00000567663.1 | n.49-1185T>G | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.624 AC: 94818AN: 151970Hom.: 30906 Cov.: 32
GnomAD3 genomes
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151970
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.624 AC: 94928AN: 152088Hom.: 30955 Cov.: 32 AF XY: 0.625 AC XY: 46448AN XY: 74334
GnomAD4 genome
?
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AC:
94928
AN:
152088
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32
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46448
AN XY:
74334
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2348
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
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