rs17321515

Positions:

• chr8-125474167-A-G
• chr8-125474167-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392

Genes affected

TRIB1AL (HGNC:56762): (TRIB1 associated lncRNA)

ACMG classification

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	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIB1AL	ENST00000522815.1	n.274+853A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73423 AN: 151888 Hom.: 17934 Cov.: 32

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

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

Other links and lift over

dbSNP: rs17321515; hg19: chr8-126486409;