Variant rs6149307 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM4BP6_ModerateBA1

The NM_001173393.3(HAVCR1):c.473_487delTGACGACTGTTCCAA(p.Met158_Pro162del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 1,593,314 control chromosomes in the GnomAD database, including 307,636 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.62 ( 24413 hom., cov: 0)

Exomes 𝑓: 0.62 ( 283223 hom. )

Consequence

HAVCR1
NM_001173393.3 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.28

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 -8 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_001173393.3.

BP6

Variant 5-157052546-GTTGGAACAGTCGTCA-G is Benign according to our data. Variant chr5-157052546-GTTGGAACAGTCGTCA-G is described in ClinVar as [Benign]. Clinvar id is 769670.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HAVCR1	NM_001173393.3 linkuse as main transcript	c.473_487delTGACGACTGTTCCAA	p.Met158_Pro162del	disruptive_inframe_deletion	4/9	ENST00000523175.6	NP_001166864.1	Q96D42B4DPB1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HAVCR1	ENST00000523175.6 linkuse as main transcript	c.473_487delTGACGACTGTTCCAA	p.Met158_Pro162del	disruptive_inframe_deletion	4/9	1	NM_001173393.3	ENSP00000427898.1		Q96D42

Frequencies

GnomAD3 genomes

AF:

0.622

AC:

83345

AN:

133918

Hom.:

24396

Cov.:

show subpopulations

Gnomad AFR

AF:

0.467

Gnomad AMI

AF:

0.795

Gnomad AMR

AF:

0.703

Gnomad ASJ

AF:

0.639

Gnomad EAS

AF:

0.820

Gnomad SAS

AF:

0.747

Gnomad FIN

AF:

0.695

Gnomad MID

AF:

0.534

Gnomad NFE

AF:

0.638

Gnomad OTH

AF:

0.628

GnomAD3 exomes

AF:

0.639

AC:

159499

AN:

249512

Hom.:

52698

AF XY:

0.640

AC XY:

86593

AN XY:

135376

show subpopulations

Gnomad AFR exome

AF:

0.331

Gnomad AMR exome

AF:

0.784

Gnomad ASJ exome

AF:

0.576

Gnomad EAS exome

AF:

0.784

Gnomad SAS exome

AF:

0.688

Gnomad FIN exome

AF:

0.652

Gnomad NFE exome

AF:

0.606

Gnomad OTH exome

AF:

0.606

GnomAD4 exome

AF:

0.619

AC:

903147

AN:

1459302

Hom.:

283223

AF XY:

0.620

AC XY:

450358

AN XY:

725954

show subpopulations

Gnomad4 AFR exome

AF:

0.321

Gnomad4 AMR exome

AF:

0.773

Gnomad4 ASJ exome

AF:

0.577

Gnomad4 EAS exome

AF:

0.825

Gnomad4 SAS exome

AF:

0.687

Gnomad4 FIN exome

AF:

0.653

Gnomad4 NFE exome

AF:

0.610

Gnomad4 OTH exome

AF:

0.599

GnomAD4 genome

AF:

0.622

AC:

83398

AN:

134012

Hom.:

24413

Cov.:

AF XY:

0.630

AC XY:

41386

AN XY:

65712

show subpopulations

Gnomad4 AFR

AF:

0.467

Gnomad4 AMR

AF:

0.704

Gnomad4 ASJ

AF:

0.639

Gnomad4 EAS

AF:

0.821

Gnomad4 SAS

AF:

0.747

Gnomad4 FIN

AF:

0.695

Gnomad4 NFE

AF:

0.638

Gnomad4 OTH

AF:

0.628

Alfa

AF:

0.505

Hom.:

2559

Asia WGS

AF:

0.700

AC:

2429

AN:

3470

EpiCase

AF:

0.596

EpiControl

AF:

0.591

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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