Genetic Variant HAVCR1:c.987-10C>A (chr5-157029851-G-T) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6BA1

The NM_001173393.3(HAVCR1):c.987-10C>A variant causes a intron change. The variant allele was found at a frequency of 0.0169 in 1,608,198 control chromosomes in the GnomAD database, including 958 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.049 ( 454 hom., cov: 31)

Exomes 𝑓: 0.014 ( 504 hom. )

Consequence

HAVCR1
NM_001173393.3 intron

Scores

Splicing: ADA: 0.6517

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 3.63

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 -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.27).

BP6

Variant 5-157029851-G-T is Benign according to our data. Variant chr5-157029851-G-T is described in ClinVar as [Benign]. Clinvar id is 3061024.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HAVCR1	NM_001173393.3 link	c.987-10C>A		intron_variant	Intron 8 of 8	ENST00000523175.6	NP_001166864.1	Q96D42B4DPB1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
HAVCR1	ENST00000523175.6 link	c.987-10C>A	intron_variant	Intron 8 of 8	1	NM_001173393.3	ENSP00000427898.1	Q96D42
HAVCR1	ENST00000339252.8 link	c.987-10C>A	intron_variant	Intron 7 of 7	1		ENSP00000344844.3	Q96D42
HAVCR1	ENST00000522693.5 link	c.953-10C>A	intron_variant	Intron 7 of 7	2		ENSP00000428524.1	E9PFX0

Frequencies

GnomAD3 genomes

AF:

0.0485

AC:

7361

AN:

151720

Hom.:

450

Cov.:

show subpopulations

Gnomad AFR

AF:

0.147

Gnomad AMI

AF:

0.0484

Gnomad AMR

AF:

0.0222

Gnomad ASJ

AF:

0.00548

Gnomad EAS

AF:

0.000387

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.00397

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0114

Gnomad OTH

AF:

0.0375

GnomAD3 exomes

AF:

0.0167

AC:

4117

AN:

246530

Hom.:

180

AF XY:

0.0142

AC XY:

1906

AN XY:

133902

show subpopulations

Gnomad AFR exome

AF:

0.145

Gnomad AMR exome

AF:

0.0116

Gnomad ASJ exome

AF:

0.00250

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00132

Gnomad FIN exome

AF:

0.00442

Gnomad NFE exome

AF:

0.0112

Gnomad OTH exome

AF:

0.0126

GnomAD4 exome

AF:

0.0136

AC:

19843

AN:

1456360

Hom.:

504

Cov.:

AF XY:

0.0129

AC XY:

9356

AN XY:

724326

show subpopulations

Gnomad4 AFR exome

AF:

0.148

Gnomad4 AMR exome

AF:

0.0126

Gnomad4 ASJ exome

AF:

0.00314

Gnomad4 EAS exome

AF:

0.0000757

Gnomad4 SAS exome

AF:

0.00137

Gnomad4 FIN exome

AF:

0.00490

Gnomad4 NFE exome

AF:

0.0115

Gnomad4 OTH exome

AF:

0.0183

GnomAD4 genome

AF:

0.0487

AC:

7391

AN:

151838

Hom.:

454

Cov.:

AF XY:

0.0460

AC XY:

3411

AN XY:

74212

show subpopulations

Gnomad4 AFR

AF:

0.147

Gnomad4 AMR

AF:

0.0219

Gnomad4 ASJ

AF:

0.00548

Gnomad4 EAS

AF:

0.000388

Gnomad4 SAS

AF:

0.00187

Gnomad4 FIN

AF:

0.00397

Gnomad4 NFE

AF:

0.0114

Gnomad4 OTH

AF:

0.0394

Alfa

AF:

0.0333

Hom.:

Bravo

AF:

0.0545

Asia WGS

AF:

0.0120

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

HAVCR1-related disorder

Benign:1

Oct 28, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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

-0.27

CADD

Benign

0.39

DANN

Benign

0.82

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.65

dbscSNV1_RF

Benign

0.54

SpliceAI score (max)

0.46

Details are displayed if max score is > 0.2

DS_AL_spliceai

0.46

Position offset: -10

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