8-125469505-A-G

Variant names:

• chr8-125469505-A-G
• rs2980875
• ENST00000522815.1:n.95+2472A>G

Variant summary

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

The ENST00000522815.1(TRIB1AL):​n.95+2472A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 151,786 control chromosomes in the GnomAD database, including 13,930 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 0.43 (13930 hom., cov: 31)
• Consequence: TRIB1AL ENST00000522815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.75
• Publications: 27 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIB1AL	NR_186610.1	n.229+2472A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIB1AL	ENST00000522815.1	n.95+2472A>G		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64545 AN: 151668 Hom.: 13909 Cov.: 31

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.426 AC: 64604 AN: 151786 Hom.: 13930 Cov.: 31 AF XY: 0.421 AC XY: 31187 AN XY: 74126

African (AFR) AF: 0.367 AC: 15202 AN: 41380

American (AMR) AF: 0.363 AC: 5533 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1283 AN: 3470

East Asian (EAS) AF: 0.524 AC: 2699 AN: 5150

South Asian (SAS) AF: 0.348 AC: 1668 AN: 4796

European-Finnish (FIN) AF: 0.468 AC: 4919 AN: 10512

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.467 AC: 31711 AN: 67934

Other (OTH) AF: 0.427 AC: 900 AN: 2108

Alfa AF: 0.356 Hom.: 2522

Bravo AF: 0.420

Asia WGS AF: 0.458 AC: 1597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.092
DANN	Benign	0.66
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs2980875; hg19: chr8-126481747;