chr5-157052312-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001173393.3(HAVCR1):​c.673+49C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 1,542,454 control chromosomes in the GnomAD database, including 320,365 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 0.60 ( 27959 hom., cov: 32)
Exomes 𝑓: 0.64 ( 292406 hom. )

Consequence

HAVCR1
NM_001173393.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.209

Publications

26 publications found
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
HAVCR1NM_001173393.3 linkc.673+49C>G intron_variant Intron 4 of 8 ENST00000523175.6 NP_001166864.1 Q96D42B4DPB1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
HAVCR1ENST00000523175.6 linkc.673+49C>G intron_variant Intron 4 of 8 1 NM_001173393.3 ENSP00000427898.1 Q96D42

Frequencies

GnomAD3 genomes
AF:
0.596
AC:
90552
AN:
151950
Hom.:
27935
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.433
Gnomad AMI
AF:
0.768
Gnomad AMR
AF:
0.690
Gnomad ASJ
AF:
0.626
Gnomad EAS
AF:
0.813
Gnomad SAS
AF:
0.750
Gnomad FIN
AF:
0.690
Gnomad MID
AF:
0.522
Gnomad NFE
AF:
0.628
Gnomad OTH
AF:
0.611
GnomAD2 exomes
AF:
0.670
AC:
162163
AN:
241998
AF XY:
0.671
show subpopulations
Gnomad AFR exome
AF:
0.433
Gnomad AMR exome
AF:
0.802
Gnomad ASJ exome
AF:
0.617
Gnomad EAS exome
AF:
0.807
Gnomad FIN exome
AF:
0.668
Gnomad NFE exome
AF:
0.629
Gnomad OTH exome
AF:
0.634
GnomAD4 exome
AF:
0.645
AC:
896183
AN:
1390386
Hom.:
292406
Cov.:
22
AF XY:
0.647
AC XY:
449502
AN XY:
694766
show subpopulations
African (AFR)
AF:
0.421
AC:
13424
AN:
31886
American (AMR)
AF:
0.790
AC:
34979
AN:
44278
Ashkenazi Jewish (ASJ)
AF:
0.618
AC:
15471
AN:
25040
East Asian (EAS)
AF:
0.841
AC:
33122
AN:
39392
South Asian (SAS)
AF:
0.738
AC:
61609
AN:
83474
European-Finnish (FIN)
AF:
0.668
AC:
35429
AN:
53030
Middle Eastern (MID)
AF:
0.544
AC:
3058
AN:
5624
European-Non Finnish (NFE)
AF:
0.631
AC:
662791
AN:
1049842
Other (OTH)
AF:
0.628
AC:
36300
AN:
57820
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.492
Heterozygous variant carriers
0
14779
29558
44338
59117
73896
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
17478
34956
52434
69912
87390
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.596
AC:
90622
AN:
152068
Hom.:
27959
Cov.:
32
AF XY:
0.605
AC XY:
44937
AN XY:
74330
show subpopulations
African (AFR)
AF:
0.433
AC:
17957
AN:
41476
American (AMR)
AF:
0.690
AC:
10542
AN:
15270
Ashkenazi Jewish (ASJ)
AF:
0.626
AC:
2174
AN:
3472
East Asian (EAS)
AF:
0.814
AC:
4206
AN:
5170
South Asian (SAS)
AF:
0.749
AC:
3617
AN:
4826
European-Finnish (FIN)
AF:
0.690
AC:
7291
AN:
10568
Middle Eastern (MID)
AF:
0.524
AC:
154
AN:
294
European-Non Finnish (NFE)
AF:
0.628
AC:
42692
AN:
67972
Other (OTH)
AF:
0.611
AC:
1290
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1814
3629
5443
7258
9072
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
768
1536
2304
3072
3840
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.549
Hom.:
3103
Bravo
AF:
0.595

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.29
DANN
Benign
0.34
PhyloP100
-0.21
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs1553318; hg19: chr5-156479323; COSMIC: COSV107447957; COSMIC: COSV107447957; API