rs2980880

Variant names:

• chr8-125468730-G-A
• rs2980880
• ENST00000522815.1:n.95+1697G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-125468730-G-A
• chr8-125468730-G-C
• chr8-125468730-G-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+1697G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.688 in 152,116 control chromosomes in the GnomAD database, including 36,035 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 0.69 (36035 hom., cov: 32)
• Consequence: TRIB1AL ENST00000522815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960
• Publications: 14 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.754 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+1697G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIB1AL	ENST00000522815.1	TSL:3	n.95+1697G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.688 AC: 104568 AN: 151998 Hom.: 35996 Cov.: 32

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.688 AC: 104661 AN: 152116 Hom.: 36035 Cov.: 32 AF XY: 0.689 AC XY: 51232 AN XY: 74348

African (AFR) AF: 0.677 AC: 28108 AN: 41492

American (AMR) AF: 0.706 AC: 10784 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1994 AN: 3466

East Asian (EAS) AF: 0.695 AC: 3600 AN: 5178

South Asian (SAS) AF: 0.775 AC: 3731 AN: 4816

European-Finnish (FIN) AF: 0.723 AC: 7651 AN: 10578

Middle Eastern (MID) AF: 0.579 AC: 169 AN: 292

European-Non Finnish (NFE) AF: 0.684 AC: 46523 AN: 67994

Other (OTH) AF: 0.664 AC: 1405 AN: 2116

Alfa AF: 0.691 Hom.: 5383

Bravo AF: 0.685

Asia WGS AF: 0.746 AC: 2594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.41
PhyloP100		0.096

Splicing

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

Other links and lift over

dbSNP: rs2980880; hg19: chr8-126480972;