5-157029720-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001173393.3(HAVCR1):c.*13C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00166 in 1,612,780 control chromosomes in the GnomAD database, including 36 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0083 ( 18 hom., cov: 31)
Exomes 𝑓: 0.00096 ( 18 hom. )
Consequence
HAVCR1
NM_001173393.3 3_prime_UTR
NM_001173393.3 3_prime_UTR
Scores
7
Clinical Significance
Conservation
PhyloP100: -0.0320
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_addAF=-0.741125).
BP6
?
Variant 5-157029720-G-T is Benign according to our data. Variant chr5-157029720-G-T is described in ClinVar as [Benign]. Clinvar id is 3037347.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00831 (1264/152042) while in subpopulation AFR AF= 0.028 (1162/41480). AF 95% confidence interval is 0.0267. There are 18 homozygotes in gnomad4. There are 597 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 18 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HAVCR1 | NM_001173393.3 | c.*13C>A | 3_prime_UTR_variant | 9/9 | ENST00000523175.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HAVCR1 | ENST00000523175.6 | c.*13C>A | 3_prime_UTR_variant | 9/9 | 1 | NM_001173393.3 | P2 | ||
HAVCR1 | ENST00000339252.8 | c.*13C>A | 3_prime_UTR_variant | 8/8 | 1 | P2 | |||
HAVCR1 | ENST00000522693.5 | c.1074C>A | p.Cys358Ter | stop_gained | 8/8 | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00827 AC: 1257AN: 151926Hom.: 18 Cov.: 31
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00215 AC: 534AN: 248422Hom.: 11 AF XY: 0.00167 AC XY: 225AN XY: 134916
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GnomAD4 exome AF: 0.000964 AC: 1408AN: 1460738Hom.: 18 Cov.: 30 AF XY: 0.000911 AC XY: 662AN XY: 726740
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GnomAD4 genome ? AF: 0.00831 AC: 1264AN: 152042Hom.: 18 Cov.: 31 AF XY: 0.00804 AC XY: 597AN XY: 74296
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
HAVCR1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 12, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MutationTaster
Benign
D;D;N;N;N
Vest4
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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