rs835036

chr1-52531568-T-Cchr1-52531568-T-G

Variant summary

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

The NM_001009881.3(TUT4):c.-93-5195A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,038 control chromosomes in the GnomAD database, including 9,167 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 0.31 (9167 hom., cov: 31)
• Consequence: TUT4 NM_001009881.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

Genes affected

TUT4 (HGNC:28981): (terminal uridylyl transferase 4) Enables RNA uridylyltransferase activity. Involved in RNA metabolic process; negative regulation of transposition, RNA-mediated; and stem cell population maintenance. Located in cytoplasmic ribonucleoprotein granule; cytosol; and nucleolus. Implicated in liver benign neoplasm. Biomarker of breast cancer. [provided by Alliance of Genome Resources, Apr 2022]

LOC105378723 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TUT4	NM_001009881.3	c.-93-5195A>G		intron_variant		ENST00000257177.9
LOC105378723	XR_001738048.2	n.118+69T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TUT4	ENST00000257177.9	c.-93-5195A>G		intron_variant		1	NM_001009881.3	P4

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46643 AN: 151920 Hom.: 9160 Cov.: 31

Gnomad AFR AF: 0.0862

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.307 AC: 46661 AN: 152038 Hom.: 9167 Cov.: 31 AF XY: 0.319 AC XY: 23720 AN XY: 74288

Gnomad4 AFR AF: 0.0860

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.724

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.342

Gnomad4 OTH AF: 0.344

Alfa AF: 0.315 Hom.: 4373

Bravo AF: 0.301

Asia WGS AF: 0.570 AC: 1983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	0.58
Dann	Benign	0.86

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

Publications

LitVar

Other links and lift over

dbSNP: rs835036; hg19: chr1-52997240;