chr9-86337398-A-C

Variant names:

• chr9-86337398-A-C
• rs10512175
• NM_024617.4:c.1455+21T>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

ENSG00000299358 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 73 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024617.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TUT7	NM_024617.4	MANE Select	c.1455+21T>G		intron	N/A	NP_078893.2
	TUT7	NM_001185059.2		c.1455+21T>G		intron	N/A	NP_001171988.1
	TUT7	NM_001185074.2		c.1086+5677T>G		intron	N/A	NP_001172003.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TUT7	ENST00000375963.8	TSL:5 MANE Select	c.1455+21T>G		intron	N/A	ENSP00000365130.3
	TUT7	ENST00000375960.6	TSL:1	c.1086+5677T>G		intron	N/A	ENSP00000365127.2
	TUT7	ENST00000375948.2	TSL:2	c.*15T>G		3_prime_UTR	Exon 5 of 5	ENSP00000365115.1

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

GnomAD2 exomes AF: 0.0255 AC: 5863 AN: 230060 AF XY: 0.0260

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 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

African (AFR) AF: 0.00467 AC: 150 AN: 32132

American (AMR) AF: 0.0177 AC: 687 AN: 38824

Ashkenazi Jewish (ASJ) AF: 0.0370 AC: 926 AN: 25036

East Asian (EAS) AF: 0.000101 AC: 4 AN: 39576

South Asian (SAS) AF: 0.0109 AC: 898 AN: 82620

European-Finnish (FIN) AF: 0.0216 AC: 1148 AN: 53174

Middle Eastern (MID) AF: 0.00529 AC: 30 AN: 5666

European-Non Finnish (NFE) AF: 0.0371 AC: 41073 AN: 1107122

Other (OTH) AF: 0.0263 AC: 1566 AN: 59596

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

African (AFR) AF: 0.00565 AC: 235 AN: 41560

American (AMR) AF: 0.0276 AC: 422 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0395 AC: 137 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5190

South Asian (SAS) AF: 0.00766 AC: 37 AN: 4828

European-Finnish (FIN) AF: 0.0216 AC: 229 AN: 10620

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0381 AC: 2594 AN: 68026

Other (OTH) AF: 0.0227 AC: 48 AN: 2114

Alfa AF: 0.0336 Hom.: 291

Bravo AF: 0.0231

Asia WGS AF: 0.00664 AC: 24 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	14
DANN	Benign	0.77
PhyloP100		5.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10512175; hg19: chr9-88952313;