8-125472284-T-G

Variant names:

• chr8-125472284-T-G
• rs2954026
• ENST00000522815.1:n.96-852T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000522815.1(TRIB1AL):​n.96-852T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,230 control chromosomes in the GnomAD database, including 44,700 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 0.76 (44700 hom., cov: 33)
• Consequence: TRIB1AL ENST00000522815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 36 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000522815.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIB1AL	NR_186610.1		n.230-852T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIB1AL	ENST00000522815.1	TSL:3	n.96-852T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115655 AN: 152112 Hom.: 44636 Cov.: 33

Gnomad AFR AF: 0.907

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.708

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.761 AC: 115778 AN: 152230 Hom.: 44700 Cov.: 33 AF XY: 0.760 AC XY: 56592 AN XY: 74420

African (AFR) AF: 0.907 AC: 37704 AN: 41566

American (AMR) AF: 0.739 AC: 11284 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2010 AN: 3468

East Asian (EAS) AF: 0.695 AC: 3601 AN: 5182

South Asian (SAS) AF: 0.786 AC: 3795 AN: 4826

European-Finnish (FIN) AF: 0.736 AC: 7790 AN: 10588

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47217 AN: 68008

Other (OTH) AF: 0.712 AC: 1501 AN: 2108

Alfa AF: 0.710 Hom.: 117693

Bravo AF: 0.765

Asia WGS AF: 0.761 AC: 2648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.9
DANN	Benign	0.75
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2954026; hg19: chr8-126484526;