chr5-157042772-G-A

Position:

• chr5-157042772-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001173393.3(HAVCR1):​c.782-90C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 775,520 control chromosomes in the GnomAD database, including 10,698 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 0.16 (2124 hom., cov: 33)
  • Exomes 𝑓: 0.16 (8574 hom.)
• Consequence: HAVCR1 NM_001173393.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HAVCR1	NM_001173393.3	c.782-90C>T		intron_variant		ENST00000523175.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HAVCR1	ENST00000523175.6	c.782-90C>T		intron_variant		1	NM_001173393.3	P2

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24928 AN: 151998 Hom.: 2127 Cov.: 33

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.171

GnomAD4 exome AF: 0.160 AC: 99922 AN: 623404 Hom.: 8574 AF XY: 0.161 AC XY: 54068 AN XY: 334816

Gnomad4 AFR exome AF: 0.170

Gnomad4 AMR exome AF: 0.0992

Gnomad4 ASJ exome AF: 0.240

Gnomad4 EAS exome AF: 0.0918

Gnomad4 SAS exome AF: 0.154

Gnomad4 FIN exome AF: 0.157

Gnomad4 NFE exome AF: 0.166

Gnomad4 OTH exome AF: 0.177

GnomAD4 genome AF: 0.164 AC: 24931 AN: 152116 Hom.: 2124 Cov.: 33 AF XY: 0.163 AC XY: 12091 AN XY: 74348

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.171

Alfa AF: 0.169 Hom.: 1984

Bravo AF: 0.164

Asia WGS AF: 0.144 AC: 501 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.73

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

LitVar

Other links and lift over

dbSNP: rs2270926; hg19: chr5-156469783; COSMIC: COSV59399575;