rs13437553

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000412306.1(TENT5A):​c.224-99405A>G 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 152,028 control chromosomes in the GnomAD database, including 3,872 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 ( 3872 hom., cov: 31)

Consequence

TENT5A
ENST00000412306.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.446
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
TENT5AENST00000412306.1 linkuse as main transcriptc.224-99405A>G intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.221
AC:
33510
AN:
151910
Hom.:
3868
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.186
Gnomad AMI
AF:
0.217
Gnomad AMR
AF:
0.256
Gnomad ASJ
AF:
0.259
Gnomad EAS
AF:
0.192
Gnomad SAS
AF:
0.179
Gnomad FIN
AF:
0.296
Gnomad MID
AF:
0.203
Gnomad NFE
AF:
0.225
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:
33534
AN:
152028
Hom.:
3872
Cov.:
31
AF XY:
0.222
AC XY:
16510
AN XY:
74284
show subpopulations
Gnomad4 AFR
AF:
0.186
Gnomad4 AMR
AF:
0.256
Gnomad4 ASJ
AF:
0.259
Gnomad4 EAS
AF:
0.192
Gnomad4 SAS
AF:
0.179
Gnomad4 FIN
AF:
0.296
Gnomad4 NFE
AF:
0.225
Gnomad4 OTH
AF:
0.231
Alfa
AF:
0.226
Hom.:
2788
Bravo
AF:
0.219
Asia WGS
AF:
0.185
AC:
642
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
3.3
DANN
Benign
0.38

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs13437553; hg19: chr6-82304235; API