rs9294233

Variant names:

• chr6-81561446-A-G
• rs9294233
• ENST00000412306.1:c.223-66333T>C

Variant summary

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

The ENST00000412306.1(TENT5A):​c.223-66333T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 151,882 control chromosomes in the GnomAD database, including 10,215 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 0.36 (10215 hom., cov: 32)
• Consequence: TENT5A ENST00000412306.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TENT5A	ENST00000412306.1	c.223-66333T>C		intron_variant	Intron 1 of 2	3		ENSP00000401884.1

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54800 AN: 151764 Hom.: 10193 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.322

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.361 AC: 54868 AN: 151882 Hom.: 10215 Cov.: 32 AF XY: 0.362 AC XY: 26824 AN XY: 74196

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.408

Alfa AF: 0.366 Hom.: 20942

Bravo AF: 0.366

Asia WGS AF: 0.401 AC: 1390 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.8
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9294233; hg19: chr6-82271163;