rs1361549

Variant names:

• chr6-81577968-G-A
• rs1361549
• ENST00000412306.1:c.223-82855C>T

Variant summary

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

The ENST00000412306.1(TENT5A):​c.223-82855C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 151,986 control chromosomes in the GnomAD database, including 8,589 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 0.30 (8589 hom., cov: 32)
• Consequence: TENT5A ENST00000412306.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.396
• Publications: 6 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

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 (NFE) allele frequency at 95% confidence interval = 0.421 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.223-82855C>T		intron_variant	Intron 1 of 2	3		ENSP00000401884.1

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45668 AN: 151868 Hom.: 8593 Cov.: 32

Gnomad AFR AF: 0.0761

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.300 AC: 45653 AN: 151986 Hom.: 8589 Cov.: 32 AF XY: 0.299 AC XY: 22221 AN XY: 74276

African (AFR) AF: 0.0760 AC: 3153 AN: 41512

American (AMR) AF: 0.313 AC: 4781 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1149 AN: 3466

East Asian (EAS) AF: 0.218 AC: 1124 AN: 5158

South Asian (SAS) AF: 0.267 AC: 1286 AN: 4822

European-Finnish (FIN) AF: 0.395 AC: 4156 AN: 10512

Middle Eastern (MID) AF: 0.295 AC: 85 AN: 288

European-Non Finnish (NFE) AF: 0.426 AC: 28903 AN: 67926

Other (OTH) AF: 0.281 AC: 594 AN: 2112

Alfa AF: 0.380 Hom.: 9211

Bravo AF: 0.285

Asia WGS AF: 0.217 AC: 751 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.56
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs1361549; hg19: chr6-82287685;