Variant 5-157032845-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001173393.3(HAVCR1):c.986+9G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 1,492,182 control chromosomes in the GnomAD database, including 47,674 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.21 ( 4110 hom., cov: 32)

Exomes 𝑓: 0.25 ( 43564 hom. )

Consequence

HAVCR1
NM_001173393.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.112

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:

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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_noAF=-0.91).

BP6

Variant 5-157032845-C-T is Benign according to our data. Variant chr5-157032845-C-T is described in ClinVar as [Benign]. Clinvar id is 3059623.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.313 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.986+9G>A		intron_variant		ENST00000523175.6

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
HAVCR1	ENST00000523175.6 linkuse as main transcript	c.986+9G>A	intron_variant	1	NM_001173393.3	P2
HAVCR1	ENST00000339252.8 linkuse as main transcript	c.986+9G>A	intron_variant	1		P2
HAVCR1	ENST00000522693.5 linkuse as main transcript	c.953-3004G>A	intron_variant	2		A2

Frequencies

GnomAD3 genomes

AF:

0.212

AC:

32266

AN:

151950

Hom.:

4109

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0740

Gnomad AMI

AF:

0.281

Gnomad AMR

AF:

0.320

Gnomad ASJ

AF:

0.272

Gnomad EAS

AF:

0.125

Gnomad SAS

AF:

0.206

Gnomad FIN

AF:

0.266

Gnomad MID

AF:

0.282

Gnomad NFE

AF:

0.266

Gnomad OTH

AF:

0.250

GnomAD3 exomes

AF:

0.250

AC:

60157

AN:

241026

Hom.:

8533

AF XY:

0.247

AC XY:

32417

AN XY:

131286

show subpopulations

Gnomad AFR exome

AF:

0.0699

Gnomad AMR exome

AF:

0.401

Gnomad ASJ exome

AF:

0.266

Gnomad EAS exome

AF:

0.128

Gnomad SAS exome

AF:

0.200

Gnomad FIN exome

AF:

0.251

Gnomad NFE exome

AF:

0.261

Gnomad OTH exome

AF:

0.266

GnomAD4 exome

AF:

0.248

AC:

332752

AN:

1340114

Hom.:

43564

Cov.:

AF XY:

0.248

AC XY:

166682

AN XY:

673224

show subpopulations

Gnomad4 AFR exome

AF:

0.0644

Gnomad4 AMR exome

AF:

0.392

Gnomad4 ASJ exome

AF:

0.265

Gnomad4 EAS exome

AF:

0.117

Gnomad4 SAS exome

AF:

0.199

Gnomad4 FIN exome

AF:

0.253

Gnomad4 NFE exome

AF:

0.257

Gnomad4 OTH exome

AF:

0.236

GnomAD4 genome

AF:

0.212

AC:

32264

AN:

152068

Hom.:

4110

Cov.:

AF XY:

0.212

AC XY:

15786

AN XY:

74304

show subpopulations

Gnomad4 AFR

AF:

0.0738

Gnomad4 AMR

AF:

0.321

Gnomad4 ASJ

AF:

0.272

Gnomad4 EAS

AF:

0.125

Gnomad4 SAS

AF:

0.206

Gnomad4 FIN

AF:

0.266

Gnomad4 NFE

AF:

0.266

Gnomad4 OTH

AF:

0.246

Alfa

AF:

0.247

Hom.:

3120

Bravo

AF:

0.214

Asia WGS

AF:

0.163

AC:

572

AN:

3478

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

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

-0.91

CADD

Benign

6.3

DANN

Benign

0.51

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

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