rs13437553

chr6-81594518-T-C

Variant summary

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

The ENST00000412306.1(TENT5A):c.224-99405A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,028 control chromosomes in the GnomAD database, including 3,872 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 0.22 (3872 hom., cov: 31)
• Consequence: TENT5A ENST00000412306.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.25 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.224-99405A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33510 AN: 151910 Hom.: 3868 Cov.: 31

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.221 AC: 33534 AN: 152028 Hom.: 3872 Cov.: 31 AF XY: 0.222 AC XY: 16510 AN XY: 74284

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.231

Alfa AF: 0.226 Hom.: 2788

Bravo AF: 0.219

Asia WGS AF: 0.185 AC: 642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.3
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13437553; hg19: chr6-82304235;