rs1276888

Variant names:

• chr6-81722671-G-A
• rs1276888
• ENST00000412306.1:c.222+28919C>T

Variant summary

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

The ENST00000412306.1(TENT5A):​c.222+28919C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0866 in 151,622 control chromosomes in the GnomAD database, including 1,012 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 0.087 (1012 hom., cov: 32)
• Consequence: TENT5A ENST00000412306.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 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.222+28919C>T		intron_variant	Intron 1 of 2	3		ENSP00000401884.1
ENSG00000232031	ENST00000793913.1	n.367+292C>T		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.0865 AC: 13098 AN: 151504 Hom.: 1012 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0162

Gnomad EAS AF: 0.0370

Gnomad SAS AF: 0.0386

Gnomad FIN AF: 0.0208

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0310

Gnomad OTH AF: 0.0719

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

GnomAD4 genome AF: 0.0866 AC: 13125 AN: 151622 Hom.: 1012 Cov.: 32 AF XY: 0.0866 AC XY: 6421 AN XY: 74108

African (AFR) AF: 0.203 AC: 8411 AN: 41380

American (AMR) AF: 0.118 AC: 1801 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.0162 AC: 56 AN: 3460

East Asian (EAS) AF: 0.0369 AC: 188 AN: 5090

South Asian (SAS) AF: 0.0384 AC: 185 AN: 4818

European-Finnish (FIN) AF: 0.0208 AC: 220 AN: 10594

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0310 AC: 2099 AN: 67750

Other (OTH) AF: 0.0712 AC: 150 AN: 2108

Alfa AF: 0.0432 Hom.: 399

Bravo AF: 0.101

Asia WGS AF: 0.0410 AC: 144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.54
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs1276888; hg19: chr6-82432388;