rs1276888

chr6-81722671-G-A

Variant summary

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

The ENST00000412306.1(TENT5A):c.223+28919C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0866 in 151,622 control chromosomes in the GnomAD database, including 1,012 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 0.087 (1012 hom., cov: 32)
• Consequence: TENT5A ENST00000412306.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540

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 (AFR) allele frequency at 95% confidence interval = 0.2 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.223+28919C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0865 AC: 13098 AN: 151504 Hom.: 1012 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0162

Gnomad EAS AF: 0.0370

Gnomad SAS AF: 0.0386

Gnomad FIN AF: 0.0208

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0310

Gnomad OTH AF: 0.0719

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

GnomAD4 genome AF: 0.0866 AC: 13125 AN: 151622 Hom.: 1012 Cov.: 32 AF XY: 0.0866 AC XY: 6421 AN XY: 74108

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0162

Gnomad4 EAS AF: 0.0369

Gnomad4 SAS AF: 0.0384

Gnomad4 FIN AF: 0.0208

Gnomad4 NFE AF: 0.0310

Gnomad4 OTH AF: 0.0712

Alfa AF: 0.0409 Hom.: 303

Bravo AF: 0.101

Asia WGS AF: 0.0410 AC: 144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.4
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1276888; hg19: chr6-82432388;