6-81718778-A-G

Variant names:

• chr6-81718778-A-G
• rs194907
• ENST00000412306.1:c.222+32812T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000412306.1(TENT5A):​c.222+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
• Publications: 1 publications found

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]

TENT5A Gene-Disease associations (from GenCC):

• osteogenesis imperfecta, type 18

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• osteogenesis imperfecta

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000232031 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412306.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TENT5A	ENST00000412306.1	TSL:3	c.222+32812T>C		intron	N/A	ENSP00000401884.1	H0Y5Y3
	ENSG00000232031	ENST00000793913.1		n.367+4185T>C		intron	N/A

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

African (AFR) AF: 0.0386 AC: 1597 AN: 41398

American (AMR) AF: 0.188 AC: 2839 AN: 15088

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 625 AN: 3440

East Asian (EAS) AF: 0.156 AC: 790 AN: 5080

South Asian (SAS) AF: 0.217 AC: 1048 AN: 4822

European-Finnish (FIN) AF: 0.197 AC: 2078 AN: 10574

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10530 AN: 67302

Other (OTH) AF: 0.145 AC: 304 AN: 2090

Alfa AF: 0.137 Hom.: 894

Bravo AF: 0.126

Asia WGS AF: 0.207 AC: 720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.79
DANN	Benign	0.50
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs194907; hg19: chr6-82428495;