rs4871603

Positions:

• chr8-125468125-C-T

Variant summary

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

The ENST00000522815.1(TRIB1AL):​n.95+1092C>T 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 0.59 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.661 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
TRIB1AL	ENST00000522815.1	n.95+1092C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.680

Gnomad4 SAS AF: 0.673

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.566

Alfa AF: 0.637 Hom.: 15654

Bravo AF: 0.583

Asia WGS AF: 0.668 AC: 2324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4871603; hg19: chr8-126480367;