chr6-81615812-T-C

Variant names:

• chr6-81615812-T-C
• rs9344208
• ENST00000412306.1:c.223-120699A>G

Variant summary

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

The ENST00000412306.1(TENT5A):​c.223-120699A>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 152,126 control chromosomes in the GnomAD database, including 3,857 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 (3857 hom., cov: 33)
• Consequence: TENT5A ENST00000412306.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102

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=-0.59).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.244 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.223-120699A>G		intron_variant	Intron 1 of 2	3		ENSP00000401884.1

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33637 AN: 152008 Hom.: 3854 Cov.: 33

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.216

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: 33667 AN: 152126 Hom.: 3857 Cov.: 33 AF XY: 0.224 AC XY: 16627 AN XY: 74348

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.215

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.232

Alfa AF: 0.222 Hom.: 7603

Bravo AF: 0.220

Asia WGS AF: 0.193 AC: 667 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	2.4
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9344208; hg19: chr6-82325529;