rs6555810

Variant names:

• chr5-157030975-T-C
• rs6555810
• NM_001173393.3:c.987-1134A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001173393.3(HAVCR1):​c.987-1134A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0492 in 151,440 control chromosomes in the GnomAD database, including 466 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 0.049 (466 hom., cov: 32)
• Consequence: HAVCR1 NM_001173393.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163
• Publications: 1 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HAVCR1	NM_001173393.3	c.987-1134A>G		intron_variant	Intron 8 of 8	ENST00000523175.6	NP_001166864.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HAVCR1	ENST00000523175.6	c.987-1134A>G		intron_variant	Intron 8 of 8	1	NM_001173393.3	ENSP00000427898.1
HAVCR1	ENST00000339252.8	c.987-1134A>G		intron_variant	Intron 7 of 7	1		ENSP00000344844.3
HAVCR1	ENST00000522693.5	c.953-1134A>G		intron_variant	Intron 7 of 7	2		ENSP00000428524.1

Frequencies

GnomAD3 genomes AF: 0.0491 AC: 7426 AN: 151340 Hom.: 462 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0227

Gnomad ASJ AF: 0.00548

Gnomad EAS AF: 0.000390

Gnomad SAS AF: 0.00167

Gnomad FIN AF: 0.00404

Gnomad MID AF: 0.00962

Gnomad NFE AF: 0.0114

Gnomad OTH AF: 0.0381

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0492 AC: 7455 AN: 151440 Hom.: 466 Cov.: 32 AF XY: 0.0466 AC XY: 3444 AN XY: 73964

African (AFR) AF: 0.149 AC: 6137 AN: 41284

American (AMR) AF: 0.0225 AC: 341 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.00548 AC: 19 AN: 3470

East Asian (EAS) AF: 0.000391 AC: 2 AN: 5120

South Asian (SAS) AF: 0.00188 AC: 9 AN: 4792

European-Finnish (FIN) AF: 0.00404 AC: 42 AN: 10386

Middle Eastern (MID) AF: 0.0104 AC: 3 AN: 288

European-Non Finnish (NFE) AF: 0.0114 AC: 774 AN: 67930

Other (OTH) AF: 0.0400 AC: 84 AN: 2098

Alfa AF: 0.0400 Hom.: 60

Bravo AF: 0.0551

Asia WGS AF: 0.0120 AC: 40 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.47
PhyloP100		-0.16
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6555810; hg19: chr5-156457986;