rs2954029

Variant names:

• chr8-125478730-A-T
• rs2954029
• ENST00000522815.1:n.274+5416A>T

Variant summary

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

The ENST00000522815.1(TRIB1AL):​n.274+5416A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,410 control chromosomes in the GnomAD database, including 13,328 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 0.42 (13328 hom., cov: 31)
• Consequence: TRIB1AL ENST00000522815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410
• Publications: 245 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.506 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.408+5416A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIB1AL	ENST00000522815.1	TSL:3	n.274+5416A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.416 AC: 62904 AN: 151298 Hom.: 13313 Cov.: 31

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.416 AC: 62952 AN: 151410 Hom.: 13328 Cov.: 31 AF XY: 0.411 AC XY: 30436 AN XY: 73966

African (AFR) AF: 0.337 AC: 13898 AN: 41262

American (AMR) AF: 0.363 AC: 5489 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1255 AN: 3464

East Asian (EAS) AF: 0.522 AC: 2695 AN: 5158

South Asian (SAS) AF: 0.349 AC: 1676 AN: 4796

European-Finnish (FIN) AF: 0.466 AC: 4851 AN: 10416

Middle Eastern (MID) AF: 0.314 AC: 91 AN: 290

European-Non Finnish (NFE) AF: 0.464 AC: 31515 AN: 67876

Other (OTH) AF: 0.423 AC: 886 AN: 2096

Alfa AF: 0.459 Hom.: 8899

Bravo AF: 0.409

Asia WGS AF: 0.454 AC: 1582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.6
DANN	Benign	0.82
PhyloP100		0.041

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2954029;

hg19: chr8-126490972;