rs4704846
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_032782.5(HAVCR2):c.*769C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 152,202 control chromosomes in the GnomAD database, including 48,581 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 0.79 ( 48581 hom., cov: 33)
Exomes 𝑓: 0.81 ( 11 hom. )
Failed GnomAD Quality Control
Consequence
HAVCR2
NM_032782.5 3_prime_UTR
NM_032782.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.256
Genes affected
HAVCR2 (HGNC:18437): (hepatitis A virus cellular receptor 2) The protein encoded by this gene belongs to the immunoglobulin superfamily, and TIM family of proteins. CD4-positive T helper lymphocytes can be divided into types 1 (Th1) and 2 (Th2) on the basis of their cytokine secretion patterns. Th1 cells are involved in cell-mediated immunity to intracellular pathogens and delayed-type hypersensitivity reactions, whereas, Th2 cells are involved in the control of extracellular helminthic infections and the promotion of atopic and allergic diseases. This protein is a Th1-specific cell surface protein that regulates macrophage activation, and inhibits Th1-mediated auto- and alloimmune responses, and promotes immunological tolerance. [provided by RefSeq, Sep 2011]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HAVCR2 | NM_032782.5 | c.*769C>T | 3_prime_UTR_variant | 7/7 | ENST00000307851.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAVCR2 | ENST00000307851.9 | c.*769C>T | 3_prime_UTR_variant | 7/7 | 1 | NM_032782.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.795 AC: 120867AN: 152084Hom.: 48548 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
120867
AN:
152084
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.813 AC: 26AN: 32Hom.: 11 Cov.: 0 AF XY: 0.818 AC XY: 18AN XY: 22
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
26
AN:
32
Hom.:
Cov.:
0
AF XY:
AC XY:
18
AN XY:
22
Gnomad4 AFR exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
GnomAD4 genome ? AF: 0.795 AC: 120952AN: 152202Hom.: 48581 Cov.: 33 AF XY: 0.803 AC XY: 59776AN XY: 74416
GnomAD4 genome
?
AF:
AC:
120952
AN:
152202
Hom.:
Cov.:
33
AF XY:
AC XY:
59776
AN XY:
74416
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
3286
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at