8-125470379-C-A

Variant names:

• chr8-125470379-C-A
• rs2954022
• ENST00000522815.1:n.96-2757C>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000522815.1(TRIB1AL):​n.96-2757C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 151,934 control chromosomes in the GnomAD database, including 13,823 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 (13823 hom., cov: 32)
• Consequence: TRIB1AL ENST00000522815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361
• Publications: 45 publications found

Genes affected

TRIB1AL (HGNC:56762): (TRIB1 associated lncRNA)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIB1AL	NR_186610.1	n.230-2757C>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIB1AL	ENST00000522815.1	n.96-2757C>A		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64323 AN: 151816 Hom.: 13803 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.424 AC: 64380 AN: 151934 Hom.: 13823 Cov.: 32 AF XY: 0.419 AC XY: 31111 AN XY: 74240

African (AFR) AF: 0.363 AC: 15026 AN: 41440

American (AMR) AF: 0.362 AC: 5526 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1255 AN: 3466

East Asian (EAS) AF: 0.525 AC: 2712 AN: 5168

South Asian (SAS) AF: 0.347 AC: 1673 AN: 4816

European-Finnish (FIN) AF: 0.467 AC: 4916 AN: 10530

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.466 AC: 31687 AN: 67948

Other (OTH) AF: 0.427 AC: 896 AN: 2100

Alfa AF: 0.440 Hom.: 28387

Bravo AF: 0.419

Asia WGS AF: 0.458 AC: 1595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	16
DANN	Benign	0.85
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs2954022; hg19: chr8-126482621;