rs7702919

Variant names:

• chr5-157059580-T-C
• rs7702919
• ENST00000699093.1:c.-12-1625A>G

Variant summary

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

The ENST00000699093.1(HAVCR1):​c.-12-1625A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 151,916 control chromosomes in the GnomAD database, including 25,850 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 0.57 (25850 hom., cov: 32)
• Consequence: HAVCR1 ENST00000699093.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 8 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HAVCR1	XM_024446020.2	c.-136-1501A>G		intron_variant	Intron 1 of 7		XP_024301788.1
HAVCR1	XM_024446021.2	c.-133-1504A>G		intron_variant	Intron 1 of 7		XP_024301789.1
HAVCR1	XM_024446023.2	c.-12-1625A>G		intron_variant	Intron 1 of 7		XP_024301791.1
HAVCR1	XM_047417097.1	c.-12-1625A>G		intron_variant	Intron 1 of 8		XP_047273053.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HAVCR1	ENST00000699093.1	c.-12-1625A>G		intron_variant	Intron 1 of 6			ENSP00000514125.1

Frequencies

GnomAD3 genomes AF: 0.573 AC: 86932 AN: 151798 Hom.: 25846 Cov.: 32

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.767

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.572 AC: 86961 AN: 151916 Hom.: 25850 Cov.: 32 AF XY: 0.575 AC XY: 42727 AN XY: 74254

African (AFR) AF: 0.417 AC: 17267 AN: 41402

American (AMR) AF: 0.589 AC: 8993 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 2372 AN: 3468

East Asian (EAS) AF: 0.845 AC: 4375 AN: 5178

South Asian (SAS) AF: 0.780 AC: 3751 AN: 4812

European-Finnish (FIN) AF: 0.551 AC: 5819 AN: 10558

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42257 AN: 67926

Other (OTH) AF: 0.593 AC: 1254 AN: 2114

Alfa AF: 0.594 Hom.: 3398

Bravo AF: 0.562

Asia WGS AF: 0.771 AC: 2680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
DANN	Benign	0.40
PhyloP100		-1.2
PromoterAI		-0.0013	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7702919; hg19: chr5-156486591; COSMIC: COSV59398741;