rs201607989

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_002218.5(ITIH4):ā€‹c.2585G>Cā€‹(p.Arg862Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000131 in 152,202 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: š‘“ 0.000013 ( 0 hom., cov: 32)

Consequence

ITIH4
NM_002218.5 missense

Scores

4
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.477
Variant links:
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 Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ITIH4NM_002218.5 linkc.2585G>C p.Arg862Pro missense_variant Exon 22 of 24 ENST00000266041.9 NP_002209.2 Q14624-1B7ZKJ8B2RMS9
ITIH4NM_001166449.2 linkc.2495G>C p.Arg832Pro missense_variant Exon 20 of 22 NP_001159921.1 Q14624-3B7ZKJ8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ITIH4ENST00000266041.9 linkc.2585G>C p.Arg862Pro missense_variant Exon 22 of 24 1 NM_002218.5 ENSP00000266041.4 Q14624-1
ENSG00000243696ENST00000468472.1 linkn.*4221G>C non_coding_transcript_exon_variant Exon 22 of 24 2 ENSP00000422253.1 D6R8Y8
ENSG00000243696ENST00000468472.1 linkn.*4221G>C 3_prime_UTR_variant Exon 22 of 24 2 ENSP00000422253.1 D6R8Y8

Frequencies

GnomAD3 genomes
AF:
0.0000131
AC:
2
AN:
152202
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000654
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD4 exome
Cov.:
32
GnomAD4 genome
AF:
0.0000131
AC:
2
AN:
152202
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
74354
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.0000654
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.51
BayesDel_addAF
Benign
-0.052
T
BayesDel_noAF
Benign
-0.31
CADD
Benign
16
DANN
Uncertain
0.99
DEOGEN2
Benign
0.097
T;T;.
Eigen
Benign
-0.53
Eigen_PC
Benign
-0.67
FATHMM_MKL
Benign
0.027
N
LIST_S2
Benign
0.82
T;T;T
M_CAP
Benign
0.015
T
MetaRNN
Uncertain
0.65
D;D;D
MetaSVM
Benign
-0.95
T
MutationAssessor
Uncertain
2.2
M;.;.
PrimateAI
Benign
0.23
T
PROVEAN
Benign
-2.1
N;N;N
REVEL
Benign
0.23
Sift
Benign
0.38
T;T;T
Sift4G
Benign
0.25
T;T;T
Polyphen
0.94
P;P;.
Vest4
0.62
MutPred
0.60
.;Loss of stability (P = 0.0188);.;
MVP
0.43
MPC
1.1
ClinPred
0.73
D
GERP RS
-2.4
Varity_R
0.45
gMVP
0.61

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs201607989; hg19: chr3-52848266; API