NM_024617.4:c.3029-39C>A

Variant names:

• chr9-86319709-G-T
• rs700760
• NM_024617.4:c.3029-39C>A

Variant summary

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

The NM_024617.4(TUT7):​c.3029-39C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 1,338,518 control chromosomes in the GnomAD database, including 224,378 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 0.63 (30897 hom., cov: 33)
  • Exomes 𝑓: 0.57 (193481 hom.)
• Consequence: TUT7 NM_024617.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.515

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TUT7	NM_024617.4	c.3029-39C>A		intron_variant	Intron 14 of 26	ENST00000375963.8	NP_078893.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TUT7	ENST00000375963.8	c.3029-39C>A		intron_variant	Intron 14 of 26	5	NM_024617.4	ENSP00000365130.3
TUT7	ENST00000375960.6	c.2509-2433C>A		intron_variant	Intron 9 of 19	1		ENSP00000365127.2
TUT7	ENST00000277141.10	c.896-39C>A		intron_variant	Intron 15 of 27	2		ENSP00000277141.6
TUT7	ENST00000375957.5	c.-197C>A		upstream_gene_variant		2		ENSP00000365124.1

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95324 AN: 151942 Hom.: 30858 Cov.: 33

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.564

GnomAD3 exomes AF: 0.576 AC: 107478 AN: 186746 Hom.: 31035 AF XY: 0.569 AC XY: 58339 AN XY: 102574

Gnomad AFR exome AF: 0.801

Gnomad AMR exome AF: 0.556

Gnomad ASJ exome AF: 0.458

Gnomad EAS exome AF: 0.541

Gnomad SAS exome AF: 0.557

Gnomad FIN exome AF: 0.640

Gnomad NFE exome AF: 0.557

Gnomad OTH exome AF: 0.546

GnomAD4 exome AF: 0.569 AC: 674932 AN: 1186458 Hom.: 193481 Cov.: 15 AF XY: 0.567 AC XY: 340275 AN XY: 600126

Gnomad4 AFR exome AF: 0.801

Gnomad4 AMR exome AF: 0.551

Gnomad4 ASJ exome AF: 0.456

Gnomad4 EAS exome AF: 0.625

Gnomad4 SAS exome AF: 0.559

Gnomad4 FIN exome AF: 0.639

Gnomad4 NFE exome AF: 0.561

Gnomad4 OTH exome AF: 0.567

GnomAD4 genome AF: 0.627 AC: 95414 AN: 152060 Hom.: 30897 Cov.: 33 AF XY: 0.630 AC XY: 46818 AN XY: 74314

Gnomad4 AFR AF: 0.792

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.562

Alfa AF: 0.497 Hom.: 2553

Bravo AF: 0.626

Asia WGS AF: 0.564 AC: 1961 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	0.62
DANN	Benign	0.44

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: rs700760; hg19: chr9-88934624;