chr8-125469835-A-G

Position:

• chr8-125469835-A-G

Variant summary

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

The ENST00000522815.1(TRIB1AL):​n.95+2802A>G 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 0.54 in 151,912 control chromosomes in the GnomAD database, including 22,440 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 0.54 (22440 hom., cov: 32)
• Consequence: TRIB1AL ENST00000522815.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920

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 (AFR) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TRIB1AL	ENST00000522815.1	n.95+2802A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81970 AN: 151794 Hom.: 22408 Cov.: 32

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.540 AC: 82052 AN: 151912 Hom.: 22440 Cov.: 32 AF XY: 0.536 AC XY: 39810 AN XY: 74254

Gnomad4 AFR AF: 0.635

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.527

Alfa AF: 0.538 Hom.: 2740

Bravo AF: 0.540

Asia WGS AF: 0.540 AC: 1879 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	2.5
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2954021; hg19: chr8-126482077;