rs10512175

chr9-86337398-A-Cchr9-86337398-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_024617.4(TUT7):c.1455+21T>G variant causes a intron change. The variant allele was found at a frequency of 0.0315 in 1,596,050 control chromosomes in the GnomAD database, including 955 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 0.024 (73 hom., cov: 32)
  • Exomes 𝑓: 0.032 (882 hom.)
• Consequence: TUT7 NM_024617.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.89

Genes affected

TUT7 (HGNC:25817): (terminal uridylyl transferase 7) Enables RNA uridylyltransferase activity and miRNA binding activity. Involved in RNA metabolic process and negative regulation of transposition, RNA-mediated. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0244 (3722/152304) while in subpopulation NFE AF= 0.0381 (2594/68026). AF 95% confidence interval is 0.0369. There are 73 homozygotes in gnomad4. There are 1786 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 73 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TUT7	NM_024617.4	c.1455+21T>G		intron_variant		ENST00000375963.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TUT7	ENST00000375963.8	c.1455+21T>G		intron_variant		5	NM_024617.4	P1
TUT7	ENST00000375960.6	c.1086+5677T>G		intron_variant		1
TUT7	ENST00000375948.2	c.*15T>G		3_prime_UTR_variant	5/5	2
TUT7	ENST00000277141.10	c.-800+21T>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0245 AC: 3722 AN: 152186 Hom.: 73 Cov.: 32

Gnomad AFR AF: 0.00567

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0276

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00766

Gnomad FIN AF: 0.0216

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0381

Gnomad OTH AF: 0.0229

GnomAD3 exomes AF: 0.0255 AC: 5863 AN: 230060 Hom.: 114 AF XY: 0.0260 AC XY: 3239 AN XY: 124602

Gnomad AFR exome AF: 0.00588

Gnomad AMR exome AF: 0.0179

Gnomad ASJ exome AF: 0.0410

Gnomad EAS exome AF: 0.000118

Gnomad SAS exome AF: 0.0106

Gnomad FIN exome AF: 0.0220

Gnomad NFE exome AF: 0.0373

Gnomad OTH exome AF: 0.0291

GnomAD4 exome AF: 0.0322 AC: 46482 AN: 1443746 Hom.: 882 Cov.: 30 AF XY: 0.0317 AC XY: 22772 AN XY: 718092

Gnomad4 AFR exome AF: 0.00467

Gnomad4 AMR exome AF: 0.0177

Gnomad4 ASJ exome AF: 0.0370

Gnomad4 EAS exome AF: 0.000101

Gnomad4 SAS exome AF: 0.0109

Gnomad4 FIN exome AF: 0.0216

Gnomad4 NFE exome AF: 0.0371

Gnomad4 OTH exome AF: 0.0263

GnomAD4 genome AF: 0.0244 AC: 3722 AN: 152304 Hom.: 73 Cov.: 32 AF XY: 0.0240 AC XY: 1786 AN XY: 74480

Gnomad4 AFR AF: 0.00565

Gnomad4 AMR AF: 0.0276

Gnomad4 ASJ AF: 0.0395

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00766

Gnomad4 FIN AF: 0.0216

Gnomad4 NFE AF: 0.0381

Gnomad4 OTH AF: 0.0227

Alfa AF: 0.0318 Hom.: 144

Bravo AF: 0.0231

Asia WGS AF: 0.00664 AC: 24 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	14
Dann	Benign	0.77

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.12		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: rs10512175; hg19: chr9-88952313;