5-157098909-AAGAG-A
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP6_Very_Strong
The NM_032782.5(HAVCR2):c.479-12_479-9del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0016 in 1,520,368 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00017 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0018 ( 0 hom. )
Consequence
HAVCR2
NM_032782.5 splice_polypyrimidine_tract, intron
NM_032782.5 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.279
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 5-157098909-AAGAG-A is Benign according to our data. Variant chr5-157098909-AAGAG-A is described in ClinVar as [Likely_benign]. Clinvar id is 2655989.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HAVCR2 | NM_032782.5 | c.479-12_479-9del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000307851.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAVCR2 | ENST00000307851.9 | c.479-12_479-9del | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_032782.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000174 AC: 26AN: 149280Hom.: 0 Cov.: 32
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GnomAD4 exome AF: 0.00176 AC: 2409AN: 1371010Hom.: 0 AF XY: 0.00179 AC XY: 1220AN XY: 682146
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GnomAD4 genome AF: 0.000174 AC: 26AN: 149358Hom.: 0 Cov.: 32 AF XY: 0.000192 AC XY: 14AN XY: 72888
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
HAVCR2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 12, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2022 | HAVCR2: BS1, BS2 - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at