chr6-81561446-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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

ENSG00000303042 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TENT5A	ENST00000412306.1	TSL:3	c.223-66333T>C		intron	N/A	ENSP00000401884.1
	ENSG00000303042	ENST00000791451.1		n.41+3351A>G		intron	N/A

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

African (AFR) AF: 0.316 AC: 13114 AN: 41446

American (AMR) AF: 0.455 AC: 6926 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1688 AN: 3470

East Asian (EAS) AF: 0.430 AC: 2208 AN: 5138

South Asian (SAS) AF: 0.324 AC: 1560 AN: 4822

European-Finnish (FIN) AF: 0.396 AC: 4178 AN: 10548

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23879 AN: 67916

Other (OTH) AF: 0.408 AC: 858 AN: 2104

Alfa AF: 0.364 Hom.: 32819

Bravo AF: 0.366

Asia WGS AF: 0.401 AC: 1390 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.8
DANN	Benign	0.60
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs9294233; hg19: chr6-82271163;