rs1039524

Variant names:

• chr3-114293427-T-A
• rs1039524
• ENST00000481065.5:c.-434T>A

Your query was ambiguous. Multiple possible variants found:

• chr3-114293427-T-A
• chr3-114293427-T-C
• chr3-114293427-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000481065.5(TIGIT):​c.-434T>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TIGIT ENST00000481065.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 0 publications found

Genes affected

TIGIT (HGNC:26838): (T cell immunoreceptor with Ig and ITIM domains) This gene encodes a member of the PVR (poliovirus receptor) family of immunoglobin proteins. The product of this gene is expressed on several classes of T cells including follicular B helper T cells (TFH). The protein has been shown to bind PVR with high affinity; this binding is thought to assist interactions between TFH and dendritic cells to regulate T cell dependent B cell responses.[provided by RefSeq, Sep 2009]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000481065.5. 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
	TIGIT	ENST00000481065.5	TSL:2	c.-434T>A		5_prime_UTR	Exon 2 of 5	ENSP00000420552.1	A0A0C4DGA4
	TIGIT	ENST00000486257.5	TSL:5	c.-62-573T>A		intron	N/A	ENSP00000419085.1	Q495A1-1
	TIGIT	ENST00000461158.5	TSL:4	c.-2-2118T>A		intron	N/A	ENSP00000418917.1	C9J0B0

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 29736 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 15970

African (AFR) AF: 0.00 AC: 0 AN: 588

American (AMR) AF: 0.00 AC: 0 AN: 3158

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 590

East Asian (EAS) AF: 0.00 AC: 0 AN: 2084

South Asian (SAS) AF: 0.00 AC: 0 AN: 3822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 972

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 64

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 17186

Other (OTH) AF: 0.00 AC: 0 AN: 1272

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.26
DANN	Benign	0.61
PhyloP100		-1.6

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1039524;

hg19: chr3-114012274;