chr5-157059492-C-G

Variant names:

• chr5-157059492-C-G
• rs41297577
• ENST00000699093.1:c.-12-1537G>C

Variant summary

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

The ENST00000699093.1(HAVCR1):​c.-12-1537G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 151,782 control chromosomes in the GnomAD database, including 6,655 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 0.27 (6655 hom., cov: 32)
• Consequence: HAVCR1 ENST00000699093.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000699093.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HAVCR1	ENST00000699093.1		c.-12-1537G>C		intron	N/A	ENSP00000514125.1	A0A8V8TPG0

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40582 AN: 151664 Hom.: 6621 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.268 AC: 40666 AN: 151782 Hom.: 6655 Cov.: 32 AF XY: 0.267 AC XY: 19831 AN XY: 74162

African (AFR) AF: 0.454 AC: 18816 AN: 41402

American (AMR) AF: 0.303 AC: 4620 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 753 AN: 3466

East Asian (EAS) AF: 0.140 AC: 720 AN: 5140

South Asian (SAS) AF: 0.169 AC: 813 AN: 4820

European-Finnish (FIN) AF: 0.218 AC: 2289 AN: 10488

Middle Eastern (MID) AF: 0.243 AC: 71 AN: 292

European-Non Finnish (NFE) AF: 0.176 AC: 11933 AN: 67928

Other (OTH) AF: 0.252 AC: 530 AN: 2104

Alfa AF: 0.0807 Hom.: 109

Bravo AF: 0.287

Asia WGS AF: 0.187 AC: 654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.94
DANN	Benign	0.34
PhyloP100		-0.64
PromoterAI		0.0070	Neutral

Splicing

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

Other links and lift over

dbSNP: rs41297577; hg19: chr5-156486503;