rs10061463

Variant names:

• chr5-157110749-A-C
• rs10061463
• ENST00000696899.1:c.-264-1502T>G

Your query was ambiguous. Multiple possible variants found:

• chr5-157110749-A-C
• chr5-157110749-A-G
• chr5-157110749-A-T

Variant summary

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

The ENST00000524219.2(HAVCR2):​c.-293-3787T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 152,162 control chromosomes in the GnomAD database, including 56,534 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 0.86 (56534 hom., cov: 32)
• Consequence: HAVCR2 ENST00000524219.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

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]

ENSG00000254246 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HAVCR2	ENST00000696899.1	c.-264-1502T>G		intron_variant	Intron 1 of 7			ENSP00000512960.1
HAVCR2	ENST00000524219.2	c.-293-3787T>G		intron_variant	Intron 1 of 6	4		ENSP00000430328.2
ENSG00000254246	ENST00000517708.1	n.148-4024A>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.861 AC: 130895 AN: 152044 Hom.: 56480 Cov.: 32

Gnomad AFR AF: 0.879

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.953

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.861 AC: 131009 AN: 152162 Hom.: 56534 Cov.: 32 AF XY: 0.867 AC XY: 64508 AN XY: 74382

Gnomad4 AFR AF: 0.879

Gnomad4 AMR AF: 0.902

Gnomad4 ASJ AF: 0.891

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.953

Gnomad4 FIN AF: 0.859

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.862

Alfa AF: 0.842 Hom.: 15748

Bravo AF: 0.865

Asia WGS AF: 0.962 AC: 3345 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	0.30
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10061463; hg19: chr5-156537760;