rs6139030

chr20-3207087-T-C

Variant summary

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

The XM_047440139.1(ITPA):c.-125-1309T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0865 in 152,138 control chromosomes in the GnomAD database, including 655 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 0.086 (655 hom., cov: 31)
• Consequence: ITPA XM_047440139.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246

Genes affected

ITPA (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITPA	XM_047440139.1	c.-125-1309T>C		intron_variant
ITPA	XM_047440140.1	c.-125-1309T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0865 AC: 13143 AN: 152020 Hom.: 654 Cov.: 31

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.0769

Gnomad AMR AF: 0.0441

Gnomad ASJ AF: 0.0720

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.0488

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0732

Gnomad OTH AF: 0.0776

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

GnomAD4 genome AF: 0.0865 AC: 13155 AN: 152138 Hom.: 655 Cov.: 31 AF XY: 0.0860 AC XY: 6397 AN XY: 74370

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.0440

Gnomad4 ASJ AF: 0.0720

Gnomad4 EAS AF: 0.181

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.0488

Gnomad4 NFE AF: 0.0732

Gnomad4 OTH AF: 0.0763

Alfa AF: 0.0778 Hom.: 952

Bravo AF: 0.0856

Asia WGS AF: 0.111 AC: 383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	5.9
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6139030; hg19: chr20-3187733;