rs17191018
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_080826.2(ISM1):c.878-393A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0496 in 152,308 control chromosomes in the GnomAD database, including 258 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 0.050 ( 258 hom., cov: 33)
Consequence
ISM1
NM_080826.2 intron
NM_080826.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.281
Genes affected
ISM1 (HGNC:16213): (isthmin 1) Predicted to be involved in negative regulation of angiogenesis. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.88).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ISM1 | NM_080826.2 | c.878-393A>G | intron_variant | ENST00000262487.5 | |||
ISM1 | XM_017027680.2 | c.877+6086A>G | intron_variant | ||||
TASP1 | XR_001754319.3 | n.1369+17421T>C | intron_variant, non_coding_transcript_variant | ||||
TASP1 | XR_007067463.1 | n.1369+17421T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ISM1 | ENST00000262487.5 | c.878-393A>G | intron_variant | 5 | NM_080826.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0496 AC: 7548AN: 152190Hom.: 258 Cov.: 33
GnomAD3 genomes
?
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152190
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0496 AC: 7550AN: 152308Hom.: 258 Cov.: 33 AF XY: 0.0513 AC XY: 3818AN XY: 74474
GnomAD4 genome
?
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AC:
7550
AN:
152308
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33
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3818
AN XY:
74474
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536
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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