6-81749628-CT-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_017633.3(TENT5A):c.*66del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 1,008,774 control chromosomes in the GnomAD database, including 592 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.066 (437 hom., cov: 30)
  • Exomes 𝑓: 0.19 (155 hom.)
• Consequence: TENT5A NM_017633.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.316

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 6-81749628-CT-C is Benign according to our data. Variant chr6-81749628-CT-C is described in ClinVar as [Benign]. Clinvar id is 1282756.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENT5A	NM_017633.3	c.*66del		3_prime_UTR_variant	3/3	ENST00000320172.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TENT5A	ENST00000320172.11	c.*66del		3_prime_UTR_variant	3/3	1	NM_017633.3	A2
TENT5A	ENST00000369754.7	c.*66del		3_prime_UTR_variant	3/3	1		P4
TENT5A	ENST00000369756.3	c.*66del		3_prime_UTR_variant	3/3	1
TENT5A	ENST00000412306.1	c.223+1961del		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0660 AC: 9209 AN: 139590 Hom.: 439 Cov.: 30

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.0229

Gnomad AMR AF: 0.0356

Gnomad ASJ AF: 0.0312

Gnomad EAS AF: 0.0170

Gnomad SAS AF: 0.0658

Gnomad FIN AF: 0.0158

Gnomad MID AF: 0.0582

Gnomad NFE AF: 0.0427

Gnomad OTH AF: 0.0608

GnomAD4 exome AF: 0.191 AC: 165862 AN: 869206 Hom.: 155 Cov.: 0 AF XY: 0.190 AC XY: 80983 AN XY: 425324

Gnomad4 AFR exome AF: 0.268

Gnomad4 AMR exome AF: 0.184

Gnomad4 ASJ exome AF: 0.202

Gnomad4 EAS exome AF: 0.198

Gnomad4 SAS exome AF: 0.189

Gnomad4 FIN exome AF: 0.176

Gnomad4 NFE exome AF: 0.188

Gnomad4 OTH exome AF: 0.207

GnomAD4 genome AF: 0.0660 AC: 9211 AN: 139568 Hom.: 437 Cov.: 30 AF XY: 0.0631 AC XY: 4260 AN XY: 67504

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.0355

Gnomad4 ASJ AF: 0.0312

Gnomad4 EAS AF: 0.0169

Gnomad4 SAS AF: 0.0661

Gnomad4 FIN AF: 0.0158

Gnomad4 NFE AF: 0.0428

Gnomad4 OTH AF: 0.0607

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 11, 2021

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs545732284; hg19: chr6-82459345;