Genetic Variant TENT5A:c.223-126958T>A (chr6-81622071-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000412306.1(TENT5A):c.223-126958T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,072 control chromosomes in the GnomAD database, including 4,064 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 0.23 ( 4064 hom., cov: 31)

Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

TENT5A
ENST00000412306.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.540

Publications

1 publications found

Variant links:

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 links:

RNA5SP210 (HGNC:43110): (RNA, 5S ribosomal pseudogene 210)

RNA5SP210 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.247 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 link	c.223-126958T>A		intron_variant	Intron 1 of 2	3		ENSP00000401884.1		H0Y5Y3
RNA5SP210	ENST00000391034.1 link	n.-129A>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.228

AC:

34606

AN:

151950

Hom.:

4062

Cov.:

show subpopulations

Gnomad AFR

AF:

0.226

Gnomad AMI

AF:

0.218

Gnomad AMR

AF:

0.253

Gnomad ASJ

AF:

0.246

Gnomad EAS

AF:

0.214

Gnomad SAS

AF:

0.182

Gnomad FIN

AF:

0.292

Gnomad MID

AF:

0.209

Gnomad NFE

AF:

0.217

Gnomad OTH

AF:

0.236

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.228

AC:

34638

AN:

152068

Hom.:

4064

Cov.:

AF XY:

0.230

AC XY:

17057

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.226

AC:

9365

AN:

41476

American (AMR)

AF:

0.253

AC:

3866

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.246

AC:

854

AN:

3472

East Asian (EAS)

AF:

0.214

AC:

1106

AN:

5160

South Asian (SAS)

AF:

0.182

AC:

880

AN:

4824

European-Finnish (FIN)

AF:

0.292

AC:

3088

AN:

10572

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.217

AC:

14725

AN:

67980

Other (OTH)

AF:

0.235

AC:

496

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1353

2707

4060

5414

6767

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

360

720

1080

1440

1800

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.131

Hom.:

221

Bravo

AF:

0.227

Asia WGS

AF:

0.196

AC:

679

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

3.7

(source)

DANN

Benign

0.51

PhyloP100

0.54

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over