rs10851132
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004791.3(ITGBL1):c.316+33085C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 151,998 control chromosomes in the GnomAD database, including 4,904 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 0.24 ( 4904 hom., cov: 32)
Consequence
ITGBL1
NM_004791.3 intron
NM_004791.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.221
Genes affected
ITGBL1 (HGNC:6164): (integrin subunit beta like 1) This gene encodes a beta integrin-related protein that is a member of the EGF-like protein family. The encoded protein contains integrin-like cysteine-rich repeats. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]
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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=-0.87).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITGBL1 | NM_004791.3 | c.316+33085C>T | intron_variant | ENST00000376180.8 | |||
ITGBL1 | NM_001271754.2 | c.-108+34254C>T | intron_variant | ||||
ITGBL1 | NM_001271755.2 | c.316+33085C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITGBL1 | ENST00000376180.8 | c.316+33085C>T | intron_variant | 1 | NM_004791.3 | P1 | |||
ITGBL1 | ENST00000618057.4 | c.316+33085C>T | intron_variant | 1 | |||||
ITGBL1 | ENST00000545560.6 | c.-108+34254C>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.241 AC: 36577AN: 151880Hom.: 4901 Cov.: 32
GnomAD3 genomes
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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: 0.241 AC: 36604AN: 151998Hom.: 4904 Cov.: 32 AF XY: 0.244 AC XY: 18142AN XY: 74278
GnomAD4 genome
?
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151998
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32
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18142
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74278
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1467
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3474
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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