rs2710323
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002215.4(ITIH1):c.688-51T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 1,596,922 control chromosomes in the GnomAD database, including 188,005 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 0.53 ( 22443 hom., cov: 31)
Exomes 𝑓: 0.47 ( 165562 hom. )
Consequence
ITIH1
NM_002215.4 intron
NM_002215.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.00
Genes affected
ITIH1 (HGNC:6166): (inter-alpha-trypsin inhibitor heavy chain 1) This gene encodes a member of the inter-alpha-trypsin inhibitor family of proteins. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the heavy chain of the inter-alpha-trypsin inhibitor complex, which is secreted by hepatocytes into the blood. The heavy chain also interacts with hyaluronan, and this interaction may play a role in ovulation and fertilization, and has been implicated in multiple inflammatory diseases. This gene is present in a gene cluster on chromosome 3. [provided by RefSeq, Nov 2015]
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITIH1 | NM_002215.4 | c.688-51T>C | intron_variant | ENST00000273283.7 | |||
ITIH1 | NM_001166434.3 | c.262-51T>C | intron_variant | ||||
ITIH1 | NM_001166435.2 | c.-177-51T>C | intron_variant | ||||
ITIH1 | NM_001166436.2 | c.-177-51T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITIH1 | ENST00000273283.7 | c.688-51T>C | intron_variant | 1 | NM_002215.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.534 AC: 81147AN: 151840Hom.: 22407 Cov.: 31
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GnomAD3 exomes AF: 0.488 AC: 119727AN: 245388Hom.: 30406 AF XY: 0.473 AC XY: 62785AN XY: 132690
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GnomAD4 exome AF: 0.474 AC: 685533AN: 1444964Hom.: 165562 Cov.: 32 AF XY: 0.469 AC XY: 335598AN XY: 716088
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GnomAD4 genome ? AF: 0.535 AC: 81245AN: 151958Hom.: 22443 Cov.: 31 AF XY: 0.530 AC XY: 39350AN XY: 74266
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ClinVar
Not reported inComputational scores
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Name
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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