rs2980880

Positions:

• chr8-125468730-G-A
• chr8-125468730-G-C
• chr8-125468730-G-T

Variant summary

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

The ENST00000522815.1(TRIB1AL):​n.95+1697G>A 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 0.688 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960

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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.754 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+1697G>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.575

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.775

Gnomad4 FIN AF: 0.723

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.664

Alfa AF: 0.692 Hom.: 5224

Bravo AF: 0.685

Asia WGS AF: 0.746 AC: 2594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2980880; hg19: chr8-126480972;