8-125495147-C-A

Variant names:

• chr8-125495147-C-A
• rs2954038
• ENST00000521991.2:n.280+8188C>A

Variant summary

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

The ENST00000521991.2(TRIB1AL):​n.280+8188C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 152,214 control chromosomes in the GnomAD database, including 44,483 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 (44483 hom., cov: 33)
• Consequence: TRIB1AL ENST00000521991.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 33 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521991.2. 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.408+21833C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIB1AL	ENST00000521991.2	TSL:2	n.280+8188C>A		intron	N/A
	TRIB1AL	ENST00000522815.1	TSL:3	n.274+21833C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115373 AN: 152096 Hom.: 44422 Cov.: 33

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.742

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.759 AC: 115491 AN: 152214 Hom.: 44483 Cov.: 33 AF XY: 0.759 AC XY: 56443 AN XY: 74406

African (AFR) AF: 0.897 AC: 37293 AN: 41556

American (AMR) AF: 0.733 AC: 11209 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1975 AN: 3470

East Asian (EAS) AF: 0.706 AC: 3648 AN: 5170

South Asian (SAS) AF: 0.779 AC: 3760 AN: 4826

European-Finnish (FIN) AF: 0.742 AC: 7859 AN: 10592

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.697 AC: 47396 AN: 67992

Other (OTH) AF: 0.700 AC: 1480 AN: 2114

Alfa AF: 0.714 Hom.: 113661

Bravo AF: 0.763

Asia WGS AF: 0.764 AC: 2658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.066
DANN	Benign	0.51
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2954038; hg19: chr8-126507389;