8-125504746-T-C

Variant names:

• chr8-125504746-T-C
• rs4512391
• ENST00000521991.2:n.280+17787T>C

Variant summary

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

The ENST00000521991.2(TRIB1AL):​n.280+17787T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 152,122 control chromosomes in the GnomAD database, including 25,353 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 0.53 (25353 hom., cov: 32)
• Consequence: TRIB1AL ENST00000521991.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 11 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.857 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIB1AL	NR_186610.1		n.408+31432T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIB1AL	ENST00000521991.2	TSL:2	n.280+17787T>C		intron	N/A
	TRIB1AL	ENST00000522815.1	TSL:3	n.274+31432T>C		intron	N/A
	TRIB1AL	ENST00000772044.1		n.71+3185T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80200 AN: 152004 Hom.: 25292 Cov.: 32

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.829

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.528 AC: 80318 AN: 152122 Hom.: 25353 Cov.: 32 AF XY: 0.526 AC XY: 39143 AN XY: 74388

African (AFR) AF: 0.864 AC: 35875 AN: 41498

American (AMR) AF: 0.452 AC: 6907 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1779 AN: 3466

East Asian (EAS) AF: 0.830 AC: 4300 AN: 5182

South Asian (SAS) AF: 0.598 AC: 2878 AN: 4814

European-Finnish (FIN) AF: 0.247 AC: 2616 AN: 10584

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24450 AN: 67984

Other (OTH) AF: 0.511 AC: 1076 AN: 2106

Alfa AF: 0.419 Hom.: 63216

Bravo AF: 0.555

Asia WGS AF: 0.735 AC: 2558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.65
PhyloP100		-0.090

Splicing

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

Other links and lift over

dbSNP: rs4512391; hg19: chr8-126516988;