dbSNP rs34333511: HAVCR1:c.-414T>A (chr5-157058357-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The ENST00000339252.8(HAVCR1):c.-414T>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0124 in 161,730 control chromosomes in the GnomAD database, including 13 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 0.013 ( 12 hom., cov: 33)

Exomes 𝑓: 0.0065 ( 1 hom. )

Consequence

HAVCR1
ENST00000339252.8 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.793

Publications

1 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]

HAVCR1 links:

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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=-0.89).

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0128 (1944/152292) while in subpopulation AFR AF = 0.0209 (869/41576). AF 95% confidence interval is 0.0197. There are 12 homozygotes in GnomAd4. There are 907 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 12 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000339252.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
HAVCR1	NM_001173393.3	MANE Select	c.-12-402T>A	intron	N/A	NP_001166864.1	Q96D42
HAVCR1	NM_001308156.2		c.-133-281T>A	intron	N/A	NP_001295085.1	E9PFX0
HAVCR1	NM_012206.3		c.-414T>A	upstream_gene	N/A	NP_036338.2	B4DPB1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
HAVCR1	ENST00000339252.8	TSL:1	c.-414T>A	5_prime_UTR	Exon 1 of 8	ENSP00000344844.3	Q96D42
HAVCR1	ENST00000523175.6	TSL:1 MANE Select	c.-12-402T>A	intron	N/A	ENSP00000427898.1	Q96D42
HAVCR1	ENST00000953674.1		c.-187T>A	5_prime_UTR	Exon 1 of 9	ENSP00000623733.1

Frequencies

GnomAD3 genomes

AF:

0.0127

AC:

1940

AN:

152174

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0209

Gnomad AMI

AF:

0.0462

Gnomad AMR

AF:

0.00995

Gnomad ASJ

AF:

0.00519

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00124

Gnomad FIN

AF:

0.00443

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0115

Gnomad OTH

AF:

0.0129

GnomAD4 exome

AF:

0.00646

AC:

AN:

9438

Hom.:

Cov.:

AF XY:

0.00543

AC XY:

AN XY:

4968

show subpopulations

African (AFR)

AF:

0.0307

AC:

AN:

228

American (AMR)

AF:

0.00521

AC:

AN:

768

Ashkenazi Jewish (ASJ)

AF:

0.00442

AC:

AN:

226

East Asian (EAS)

AF:

0.00

AC:

AN:

430

South Asian (SAS)

AF:

0.00

AC:

AN:

848

European-Finnish (FIN)

AF:

0.00286

AC:

AN:

350

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00698

AC:

AN:

6020

Other (OTH)

AF:

0.0112

AC:

AN:

538

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.0128

AC:

1944

AN:

152292

Hom.:

Cov.:

AF XY:

0.0122

AC XY:

907

AN XY:

74458

show subpopulations

African (AFR)

AF:

0.0209

AC:

869

AN:

41576

American (AMR)

AF:

0.00987

AC:

151

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.00519

AC:

AN:

3470

East Asian (EAS)

AF:

0.000193

AC:

AN:

5174

South Asian (SAS)

AF:

0.00124

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.00443

AC:

AN:

10618

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0115

AC:

779

AN:

68018

Other (OTH)

AF:

0.0147

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

101

201

302

402

503

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

110

<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:

0.0128

Hom.:

Bravo

AF:

0.0130

Asia WGS

AF:

0.00404

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.9

(source)

DANN

Benign

0.84

PhyloP100

-0.79

PromoterAI

-0.013

Neutral

(source)

Mutation Taster

=300/0

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over