rs1917063

Variant names:

• chr6-81613490-C-T
• rs1917063
• ENST00000412306.1:c.223-118377G>A

Variant summary

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

The ENST00000412306.1(TENT5A):​c.223-118377G>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
• Publications: 4 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=-0.89).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TENT5A	ENST00000412306.1	c.223-118377G>A		intron_variant	Intron 1 of 2	3		ENSP00000401884.1

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

African (AFR) AF: 0.204 AC: 8450 AN: 41410

American (AMR) AF: 0.250 AC: 3811 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 854 AN: 3470

East Asian (EAS) AF: 0.214 AC: 1104 AN: 5148

South Asian (SAS) AF: 0.179 AC: 861 AN: 4812

European-Finnish (FIN) AF: 0.292 AC: 3064 AN: 10498

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14688 AN: 67920

Other (OTH) AF: 0.231 AC: 488 AN: 2108

Alfa AF: 0.224 Hom.: 1920

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
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs1917063; hg19: chr6-82323207;