rs2066411

chr1-117624128-A-Gchr1-117624128-A-T

Variant summary

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

The NM_017709.4(TENT5C):c.*84A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 1,159,988 control chromosomes in the GnomAD database, including 31,647 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 0.24 (4086 hom., cov: 29)
  • Exomes 𝑓: 0.23 (27561 hom.)
• Consequence: TENT5C NM_017709.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.16

Genes affected

TENT5C (HGNC:24712): (terminal nucleotidyltransferase 5C) Enables RNA adenylyltransferase activity. Involved in mRNA stabilization. Located in cytoplasm 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=-0.52).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENT5C	NM_017709.4	c.*84A>G		3_prime_UTR_variant	2/2	ENST00000369448.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TENT5C	ENST00000369448.4	c.*84A>G		3_prime_UTR_variant	2/2	1	NM_017709.4	P1

Frequencies

GnomAD3 genomes AF: 0.237 AC: 34981 AN: 147724 Hom.: 4083 Cov.: 29

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.292

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.268

GnomAD4 exome AF: 0.230 AC: 233007 AN: 1012222 Hom.: 27561 Cov.: 14 AF XY: 0.233 AC XY: 116822 AN XY: 501054

Gnomad4 AFR exome AF: 0.196

Gnomad4 AMR exome AF: 0.321

Gnomad4 ASJ exome AF: 0.299

Gnomad4 EAS exome AF: 0.206

Gnomad4 SAS exome AF: 0.308

Gnomad4 FIN exome AF: 0.220

Gnomad4 NFE exome AF: 0.222

Gnomad4 OTH exome AF: 0.246

GnomAD4 genome AF: 0.237 AC: 34992 AN: 147766 Hom.: 4086 Cov.: 29 AF XY: 0.244 AC XY: 17486 AN XY: 71712

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.320

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.267

Alfa AF: 0.226 Hom.: 4581

Bravo AF: 0.236

Asia WGS AF: 0.247 AC: 856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
Cadd	Benign	14
Dann	Benign	0.87

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: rs2066411; hg19: chr1-118166750; COSMIC: COSV65616308;