rs545732284

Variant names:

• chr6-81749628-CTTTTTTTTTTTT-C
• rs545732284
• NM_017633.3:c.*55_*66delAAAAAAAAAAAA

Your query was ambiguous. Multiple possible variants found:

• chr6-81749628-CTTTTTTTTTTTT-C
• chr6-81749628-CTTTTTTTTTTTT-CT
• chr6-81749628-CTTTTTTTTTTTT-CTT
• chr6-81749628-CTTTTTTTTTTTT-CTTT
• chr6-81749628-CTTTTTTTTTTTT-CTTTT
• chr6-81749628-CTTTTTTTTTTTT-CTTTTT
• chr6-81749628-CTTTTTTTTTTTT-CTTTTTT
• chr6-81749628-CTTTTTTTTTTTT-CTTTTTTT
• chr6-81749628-CTTTTTTTTTTTT-CTTTTTTTT
• chr6-81749628-CTTTTTTTTTTTT-CTTTTTTTTT
• chr6-81749628-CTTTTTTTTTTTT-CTTTTTTTTTT
• chr6-81749628-CTTTTTTTTTTTT-CTTTTTTTTTTT
• chr6-81749628-CTTTTTTTTTTTT-CTTTTTTTTTTTTT
• chr6-81749628-CTTTTTTTTTTTT-CTTTTTTTTTTTTTT
• chr6-81749628-CTTTTTTTTTTTT-CTTTTTTTTTTTTTTT
• chr6-81749628-CTTTTTTTTTTTT-CTTTTTTTTTTTTTTTT
• chr6-81749628-CTTTTTTTTTTTT-CTTTTTTTTTTTTTTTTT
• chr6-81749628-CTTTTTTTTTTTT-CTTTTTTTTTTTTTTTTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_017633.3(TENT5A):​c.*55_*66delAAAAAAAAAAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000716 in 139,756 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0000072 (0 hom., cov: 30)
• Consequence: TENT5A NM_017633.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0510
• 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

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017633.3. 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
	TENT5A	NM_017633.3	MANE Select	c.*55_*66delAAAAAAAAAAAA		3_prime_UTR	Exon 3 of 3	NP_060103.2	Q96IP4-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TENT5A	ENST00000320172.11	TSL:1 MANE Select	c.*55_*66delAAAAAAAAAAAA		3_prime_UTR	Exon 3 of 3	ENSP00000318298.6	Q96IP4-1
	TENT5A	ENST00000369756.3	TSL:1	c.*55_*66delAAAAAAAAAAAA		3_prime_UTR	Exon 3 of 3	ENSP00000358771.3	Q5TF85
	TENT5A	ENST00000369754.7	TSL:1	c.*55_*66delAAAAAAAAAAAA		3_prime_UTR	Exon 3 of 3	ENSP00000358769.3	Q96IP4-2

Frequencies

GnomAD3 genomes AF: 0.00000716 AC: 1 AN: 139756 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000156

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.00000716 AC: 1 AN: 139756 Hom.: 0 Cov.: 30 AF XY: 0.0000148 AC XY: 1 AN XY: 67592

African (AFR) AF: 0.00 AC: 0 AN: 38028

American (AMR) AF: 0.00 AC: 0 AN: 14012

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3300

East Asian (EAS) AF: 0.00 AC: 0 AN: 4816

South Asian (SAS) AF: 0.00 AC: 0 AN: 4380

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8262

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.0000156 AC: 1 AN: 63898

Other (OTH) AF: 0.00 AC: 0 AN: 1896

Alfa AF: 0.00 Hom.: 2

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.051

Splicing

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

Other links and lift over

dbSNP: rs545732284; hg19: chr6-82459345;