rs3810560

chr20-3227173-T-C

Variant summary

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

The NM_001324240.2(ITPA):c.*485T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,246 control chromosomes in the GnomAD database, including 10,953 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 0.35 (10953 hom., cov: 34)
• Consequence: ITPA NM_001324240.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

ITPA (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ITPA	NM_001324240.2	c.*485T>C		3_prime_UTR_variant	7/7

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52884 AN: 152128 Hom.: 10950 Cov.: 34

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.487

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.347 AC: 52892 AN: 152246 Hom.: 10953 Cov.: 34 AF XY: 0.353 AC XY: 26267 AN XY: 74424

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.487

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.651

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.369

Alfa AF: 0.429 Hom.: 7786

Bravo AF: 0.330

Asia WGS AF: 0.557 AC: 1936 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	1.8
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3810560; hg19: chr20-3207819;