rs4871603

Variant names:

• chr8-125468125-C-T
• rs4871603
• ENST00000522815.1:n.95+1092C>T

Variant summary

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

The ENST00000522815.1(TRIB1AL):​n.95+1092C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 152,078 control chromosomes in the GnomAD database, including 26,980 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 0.59 (26980 hom., cov: 33)
• Consequence: TRIB1AL ENST00000522815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 17 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.661 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIB1AL	NR_186610.1		n.229+1092C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIB1AL	ENST00000522815.1	TSL:3	n.95+1092C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89624 AN: 151960 Hom.: 26954 Cov.: 33

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.590 AC: 89694 AN: 152078 Hom.: 26980 Cov.: 33 AF XY: 0.589 AC XY: 43819 AN XY: 74334

African (AFR) AF: 0.453 AC: 18804 AN: 41482

American (AMR) AF: 0.601 AC: 9174 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1845 AN: 3468

East Asian (EAS) AF: 0.680 AC: 3521 AN: 5178

South Asian (SAS) AF: 0.673 AC: 3248 AN: 4826

European-Finnish (FIN) AF: 0.657 AC: 6951 AN: 10574

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44127 AN: 67974

Other (OTH) AF: 0.566 AC: 1194 AN: 2110

Alfa AF: 0.635 Hom.: 17336

Bravo AF: 0.583

Asia WGS AF: 0.668 AC: 2324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.73
DANN	Benign	0.78
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4871603; hg19: chr8-126480367;