Variant chr5-157052413-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001173393.3(HAVCR1):c.621T>G(p.Thr207=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.857 in 1,613,720 control chromosomes in the GnomAD database, including 594,257 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.87 ( 57539 hom., cov: 34)

Exomes 𝑓: 0.86 ( 536718 hom. )

Consequence

HAVCR1
NM_001173393.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -3.27

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]

HAVCR1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.04).

BP6

Variant 5-157052413-A-C is Benign according to our data. Variant chr5-157052413-A-C is described in ClinVar as [Benign]. Clinvar id is 3059346.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-3.27 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HAVCR1	NM_001173393.3 linkuse as main transcript	c.621T>G	p.Thr207=	synonymous_variant	4/9	ENST00000523175.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HAVCR1	ENST00000523175.6 linkuse as main transcript	c.621T>G	p.Thr207=	synonymous_variant	4/9	1	NM_001173393.3	P2

Frequencies

GnomAD3 genomes

AF:

0.869

AC:

132164

AN:

152138

Hom.:

57488

Cov.:

show subpopulations

Gnomad AFR

AF:

0.876

Gnomad AMI

AF:

0.984

Gnomad AMR

AF:

0.911

Gnomad ASJ

AF:

0.908

Gnomad EAS

AF:

0.987

Gnomad SAS

AF:

0.950

Gnomad FIN

AF:

0.857

Gnomad MID

AF:

0.870

Gnomad NFE

AF:

0.838

Gnomad OTH

AF:

0.876

GnomAD3 exomes

AF:

0.884

AC:

220762

AN:

249590

Hom.:

98030

AF XY:

0.886

AC XY:

119983

AN XY:

135406

show subpopulations

Gnomad AFR exome

AF:

0.880

Gnomad AMR exome

AF:

0.936

Gnomad ASJ exome

AF:

0.902

Gnomad EAS exome

AF:

0.989

Gnomad SAS exome

AF:

0.956

Gnomad FIN exome

AF:

0.846

Gnomad NFE exome

AF:

0.840

Gnomad OTH exome

AF:

0.869

GnomAD4 exome

AF:

0.856

AC:

1250808

AN:

1461464

Hom.:

536718

Cov.:

AF XY:

0.859

AC XY:

624204

AN XY:

727046

show subpopulations

Gnomad4 AFR exome

AF:

0.878

Gnomad4 AMR exome

AF:

0.932

Gnomad4 ASJ exome

AF:

0.904

Gnomad4 EAS exome

AF:

0.982

Gnomad4 SAS exome

AF:

0.954

Gnomad4 FIN exome

AF:

0.846

Gnomad4 NFE exome

AF:

0.839

Gnomad4 OTH exome

AF:

0.865

GnomAD4 genome

AF:

0.869

AC:

132272

AN:

152256

Hom.:

57539

Cov.:

AF XY:

0.872

AC XY:

64945

AN XY:

74436

show subpopulations

Gnomad4 AFR

AF:

0.876

Gnomad4 AMR

AF:

0.912

Gnomad4 ASJ

AF:

0.908

Gnomad4 EAS

AF:

0.987

Gnomad4 SAS

AF:

0.950

Gnomad4 FIN

AF:

0.857

Gnomad4 NFE

AF:

0.838

Gnomad4 OTH

AF:

0.875

Alfa

AF:

0.850

Hom.:

66007

Bravo

AF:

0.873

EpiCase

AF:

0.847

EpiControl

AF:

0.845

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

HAVCR1-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 17, 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: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.28

DANN

Benign

0.34

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over