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GeneBe

rs17321515

Variant summary

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

The ENST00000522815.1(TRIB1AL):n.274+853A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 152,006 control chromosomes in the GnomAD database, including 17,963 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 0.48 ( 17963 hom., cov: 32)

Consequence

TRIB1AL
ENST00000522815.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.392
Variant links:
Genes affected
TRIB1AL (HGNC:56762): (TRIB1 associated lncRNA)

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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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.546 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
TRIB1ALENST00000522815.1 linkuse as main transcriptn.274+853A>G intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.483
AC:
73423
AN:
151888
Hom.:
17934
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.552
Gnomad AMI
AF:
0.655
Gnomad AMR
AF:
0.395
Gnomad ASJ
AF:
0.367
Gnomad EAS
AF:
0.521
Gnomad SAS
AF:
0.352
Gnomad FIN
AF:
0.468
Gnomad MID
AF:
0.348
Gnomad NFE
AF:
0.475
Gnomad OTH
AF:
0.472
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.483
AC:
73494
AN:
152006
Hom.:
17963
Cov.:
32
AF XY:
0.477
AC XY:
35443
AN XY:
74310
show subpopulations
Gnomad4 AFR
AF:
0.552
Gnomad4 AMR
AF:
0.395
Gnomad4 ASJ
AF:
0.367
Gnomad4 EAS
AF:
0.521
Gnomad4 SAS
AF:
0.350
Gnomad4 FIN
AF:
0.468
Gnomad4 NFE
AF:
0.475
Gnomad4 OTH
AF:
0.480
Alfa
AF:
0.474
Hom.:
8449
Bravo
AF:
0.486
Asia WGS
AF:
0.472
AC:
1643
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
Cadd
Benign
3.8
Dann
Benign
0.64

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: rs17321515; hg19: chr8-126486409; API