rs34333511
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000339252.8(HAVCR1):c.-414T>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0124 in 161,730 control chromosomes in the GnomAD database, including 13 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 0.013 ( 12 hom., cov: 33)
Exomes 𝑓: 0.0065 ( 1 hom. )
Consequence
HAVCR1
ENST00000339252.8 5_prime_UTR
ENST00000339252.8 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.793
Genes affected
HAVCR1 (HGNC:17866): (hepatitis A virus cellular receptor 1) The protein encoded by this gene is a membrane receptor for both human hepatitis A virus (HHAV) and TIMD4. The encoded protein may be involved in the moderation of asthma and allergic diseases. The reference genome represents an allele that retains a MTTVP amino acid segment that confers protection against atopy in HHAV seropositive individuals. The protein is a receptor for multiple other viruses, including Ebola virus, Marburg virus, Dengue virus, and Zika virus and is a possible entry factor for SARS-CoV-2 and other coronaviruses. [provided by RefSeq, Sep 2021]
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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).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0128 (1944/152292) while in subpopulation AFR AF= 0.0209 (869/41576). AF 95% confidence interval is 0.0197. There are 12 homozygotes in gnomad4. There are 907 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 12 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HAVCR1 | NM_001173393.3 | c.-12-402T>A | intron_variant | ENST00000523175.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAVCR1 | ENST00000523175.6 | c.-12-402T>A | intron_variant | 1 | NM_001173393.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0127 AC: 1940AN: 152174Hom.: 12 Cov.: 33
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GnomAD4 exome AF: 0.00646 AC: 61AN: 9438Hom.: 1 Cov.: 0 AF XY: 0.00543 AC XY: 27AN XY: 4968
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GnomAD4 genome ? AF: 0.0128 AC: 1944AN: 152292Hom.: 12 Cov.: 33 AF XY: 0.0122 AC XY: 907AN XY: 74458
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at