rs4687554
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002218.5(ITIH4):c.90+434A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 346,970 control chromosomes in the GnomAD database, including 10,272 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 0.25 ( 4863 hom., cov: 34)
Exomes 𝑓: 0.22 ( 5409 hom. )
Consequence
ITIH4
NM_002218.5 intron
NM_002218.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0520
Genes affected
ITIH4 (HGNC:6169): (inter-alpha-trypsin inhibitor heavy chain 4) The protein encoded by this gene is secreted into the blood, where it is cleaved by plasma kallikrein into two smaller forms. Expression of this gene has been detected only in liver, and it seems to be upregulated during surgical trauma. This gene is part of a cluster of similar genes on chromosome 3. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2009]
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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=-0.89).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ITIH4 | NM_002218.5 | c.90+434A>G | intron_variant | ENST00000266041.9 | |||
ITIH4 | NM_001166449.2 | c.90+434A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ITIH4 | ENST00000266041.9 | c.90+434A>G | intron_variant | 1 | NM_002218.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.246 AC: 37354AN: 152102Hom.: 4862 Cov.: 34
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GnomAD4 exome AF: 0.221 AC: 43083AN: 194750Hom.: 5409 Cov.: 0 AF XY: 0.207 AC XY: 22062AN XY: 106616
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GnomAD4 genome ? AF: 0.246 AC: 37379AN: 152220Hom.: 4863 Cov.: 34 AF XY: 0.247 AC XY: 18422AN XY: 74434
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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