rs10849033

Variant names:

• chr12-4315956-G-A
• rs10849033
• ENST00000674624.1:n.720+26966G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-4315956-G-A
• chr12-4315956-G-T

Variant summary

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

The ENST00000674624.1(ENSG00000285901):​n.720+26966G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 152,228 control chromosomes in the GnomAD database, including 55,595 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 0.83 (55595 hom., cov: 34)
• Consequence: ENSG00000285901 ENST00000674624.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.713
• Publications: 12 publications found

Genes affected

ENSG00000285901 (HGNC:):

TIGAR (HGNC:1185): (TP53 induced glycolysis regulatory phosphatase) This gene is regulated as part of the p53 tumor suppressor pathway and encodes a protein with sequence similarity to the bisphosphate domain of the glycolytic enzyme that degrades fructose-2,6-bisphosphate. The protein functions by blocking glycolysis and directing the pathway into the pentose phosphate shunt. Expression of this protein also protects cells from DNA damaging reactive oxygen species and provides some protection from DNA damage-induced apoptosis. The 12p13.32 region that includes this gene is paralogous to the 11q13.3 region. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.977 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
ENSG00000285901	ENST00000674624.1	n.720+26966G>A		intron_variant	Intron 4 of 9			ENSP00000501898.1
TIGAR	ENST00000635110.1	c.-146+7200G>A		intron_variant	Intron 1 of 5	5		ENSP00000488928.1
ENSG00000285901	ENST00000648100.1	n.721-15324G>A		intron_variant	Intron 4 of 11			ENSP00000497536.1

Frequencies

GnomAD3 genomes AF: 0.835 AC: 126960 AN: 152110 Hom.: 55605 Cov.: 34

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.985

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.973

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.864

Gnomad FIN AF: 0.957

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.983

Gnomad OTH AF: 0.857

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

GnomAD4 genome AF: 0.834 AC: 126981 AN: 152228 Hom.: 55595 Cov.: 34 AF XY: 0.831 AC XY: 61870 AN XY: 74420

African (AFR) AF: 0.579 AC: 24029 AN: 41486

American (AMR) AF: 0.826 AC: 12637 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.973 AC: 3377 AN: 3472

East Asian (EAS) AF: 0.527 AC: 2730 AN: 5176

South Asian (SAS) AF: 0.865 AC: 4178 AN: 4828

European-Finnish (FIN) AF: 0.957 AC: 10156 AN: 10608

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.983 AC: 66897 AN: 68048

Other (OTH) AF: 0.853 AC: 1801 AN: 2112

Alfa AF: 0.919 Hom.: 148672

Bravo AF: 0.810

Asia WGS AF: 0.677 AC: 2357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.58
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs10849033; hg19: chr12-4425122;