rs1361549

chr6-81577968-G-A

Variant summary

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

The ENST00000412306.1(TENT5A):c.224-82855C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 151,986 control chromosomes in the GnomAD database, including 8,589 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 0.30 (8589 hom., cov: 32)
• Consequence: TENT5A ENST00000412306.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.396

Genes affected

TENT5A (HGNC:18345): (terminal nucleotidyltransferase 5A) Enables RNA binding activity. Predicted to be involved in mRNA stabilization. Predicted to act upstream of or within response to bacterium. Implicated in lung non-small cell carcinoma; osteoarthritis; and osteogenesis imperfecta type 18. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TENT5A	ENST00000412306.1	c.224-82855C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45668 AN: 151868 Hom.: 8593 Cov.: 32

Gnomad AFR AF: 0.0761

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.300 AC: 45653 AN: 151986 Hom.: 8589 Cov.: 32 AF XY: 0.299 AC XY: 22221 AN XY: 74276

Gnomad4 AFR AF: 0.0760

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.281

Alfa AF: 0.381 Hom.: 4986

Bravo AF: 0.285

Asia WGS AF: 0.217 AC: 751 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.7
Dann	Benign	0.56

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1361549; hg19: chr6-82287685;