6-81613490-C-T

Position:

• chr6-81613490-C-T

Variant summary

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

The ENST00000412306.1(TENT5A):​c.224-118377G>A 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 151,798 control chromosomes in the GnomAD database, including 3,845 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 (3845 hom., cov: 31)
• Consequence: TENT5A ENST00000412306.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209

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=-0.89).
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TENT5A	ENST00000412306.1	c.224-118377G>A		intron_variant		3		ENSP00000401884

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33547 AN: 151684 Hom.: 3842 Cov.: 31

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.217

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: 33575 AN: 151798 Hom.: 3845 Cov.: 31 AF XY: 0.223 AC XY: 16562 AN XY: 74132

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.231

Alfa AF: 0.225 Hom.: 1136

Bravo AF: 0.220

Asia WGS AF: 0.192 AC: 666 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.61
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1917063; hg19: chr6-82323207;