5-157098909-AAGAGAGAGAG-AAGAGAGAG

Variant names:

• chr5-157098909-AAG-A
• rs70984443
• NM_032782.5:c.479-10_479-9delCT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_032782.5(HAVCR2):​c.479-10_479-9delCT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00143 in 147,944 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0014 (0 hom., cov: 32)
  • Exomes 𝑓: 0.21 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: HAVCR2 NM_032782.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228

Genes affected

HAVCR2 (HGNC:18437): (hepatitis A virus cellular receptor 2) The protein encoded by this gene belongs to the immunoglobulin superfamily, and TIM family of proteins. CD4-positive T helper lymphocytes can be divided into types 1 (Th1) and 2 (Th2) on the basis of their cytokine secretion patterns. Th1 cells are involved in cell-mediated immunity to intracellular pathogens and delayed-type hypersensitivity reactions, whereas, Th2 cells are involved in the control of extracellular helminthic infections and the promotion of atopic and allergic diseases. This protein is a Th1-specific cell surface protein that regulates macrophage activation, and inhibits Th1-mediated auto- and alloimmune responses, and promotes immunological tolerance. [provided by RefSeq, Sep 2011]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HAVCR2	NM_032782.5	c.479-10_479-9delCT		intron_variant	Intron 3 of 6	ENST00000307851.9	NP_116171.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HAVCR2	ENST00000307851.9	c.479-10_479-9delCT		intron_variant	Intron 3 of 6	1	NM_032782.5	ENSP00000312002.4

Frequencies

GnomAD3 genomes AF: 0.00143 AC: 211 AN: 147880 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000883

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00142

Gnomad ASJ AF: 0.000882

Gnomad EAS AF: 0.000195

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00601

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00137

Gnomad OTH AF: 0.00150

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.210 AC: 220311 AN: 1048240 Hom.: 0 AF XY: 0.219 AC XY: 112895 AN XY: 515944

Gnomad4 AFR exome AF: 0.219

Gnomad4 AMR exome AF: 0.275

Gnomad4 ASJ exome AF: 0.282

Gnomad4 EAS exome AF: 0.299

Gnomad4 SAS exome AF: 0.294

Gnomad4 FIN exome AF: 0.254

Gnomad4 NFE exome AF: 0.195

Gnomad4 OTH exome AF: 0.229

GnomAD4 genome AF: 0.00143 AC: 212 AN: 147944 Hom.: 0 Cov.: 32 AF XY: 0.00157 AC XY: 113 AN XY: 72048

Gnomad4 AFR AF: 0.000881

Gnomad4 AMR AF: 0.00142

Gnomad4 ASJ AF: 0.000882

Gnomad4 EAS AF: 0.000195

Gnomad4 SAS AF: 0.000212

Gnomad4 FIN AF: 0.00601

Gnomad4 NFE AF: 0.00137

Gnomad4 OTH AF: 0.00148

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs70984443; hg19: chr5-156525920;