rs10485393

Variant names:

• chr6-81494795-G-C
• rs10485393
• ENST00000412306.1:c.*38+239C>G

Variant summary

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

The ENST00000412306.1(TENT5A):​c.*38+239C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0414 in 152,088 control chromosomes in the GnomAD database, including 128 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 0.041 (128 hom., cov: 31)
• Consequence: TENT5A ENST00000412306.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.177
• Publications: 0 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

ENSG00000298959 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0536 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.*38+239C>G		intron	N/A	ENSP00000401884.1
	ENSG00000298959	ENST00000759357.1		n.199+18934C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0414 AC: 6287 AN: 151970 Hom.: 127 Cov.: 31

Gnomad AFR AF: 0.0554

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0265

Gnomad ASJ AF: 0.00836

Gnomad EAS AF: 0.0535

Gnomad SAS AF: 0.0375

Gnomad FIN AF: 0.0271

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0401

Gnomad OTH AF: 0.0334

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

GnomAD4 genome AF: 0.0414 AC: 6298 AN: 152088 Hom.: 128 Cov.: 31 AF XY: 0.0401 AC XY: 2984 AN XY: 74362

African (AFR) AF: 0.0555 AC: 2304 AN: 41502

American (AMR) AF: 0.0265 AC: 405 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.00836 AC: 29 AN: 3470

East Asian (EAS) AF: 0.0535 AC: 276 AN: 5162

South Asian (SAS) AF: 0.0367 AC: 177 AN: 4820

European-Finnish (FIN) AF: 0.0271 AC: 287 AN: 10576

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0401 AC: 2729 AN: 67978

Other (OTH) AF: 0.0345 AC: 73 AN: 2116

Alfa AF: 0.0463 Hom.: 25

Bravo AF: 0.0405

Asia WGS AF: 0.0420 AC: 146 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.31
DANN	Benign	0.39
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs10485393; hg19: chr6-82204512;