6-81718778-A-G

Variant summary

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

The ENST00000412306.1(TENT5A):c.223+32812T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 150,996 control chromosomes in the GnomAD database, including 1,607 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 0.13 (1607 hom., cov: 32)
• Consequence: TENT5A ENST00000412306.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.647

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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.206 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+32812T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20068 AN: 150878 Hom.: 1606 Cov.: 32

Gnomad AFR AF: 0.0386

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.133 AC: 20076 AN: 150996 Hom.: 1607 Cov.: 32 AF XY: 0.138 AC XY: 10159 AN XY: 73734

Gnomad4 AFR AF: 0.0386

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.145

Alfa AF: 0.136 Hom.: 796

Bravo AF: 0.126

Asia WGS AF: 0.207 AC: 720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.79
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs194907; hg19: chr6-82428495;