chr8-125527809-G-A

Variant names:

• chr8-125527809-G-A
• rs1551398
• ENST00000521991.2:n.608-2132G>A

Variant summary

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

The ENST00000521991.2(TRIB1AL):​n.608-2132G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 152,102 control chromosomes in the GnomAD database, including 21,013 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 0.48 (21013 hom., cov: 32)
• Consequence: TRIB1AL ENST00000521991.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210
• Publications: 49 publications found

Genes affected

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

LINC02964 (HGNC:53487): (long intergenic non-protein coding RNA 2964)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.618 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.409-13101G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIB1AL	ENST00000521991.2	TSL:2	n.608-2132G>A		intron	N/A
	TRIB1AL	ENST00000522815.1	TSL:3	n.275-13101G>A		intron	N/A
	TRIB1AL	ENST00000772044.1		n.690+4796G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73366 AN: 151984 Hom.: 21007 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.743

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.482 AC: 73374 AN: 152102 Hom.: 21013 Cov.: 32 AF XY: 0.486 AC XY: 36180 AN XY: 74372

African (AFR) AF: 0.176 AC: 7309 AN: 41476

American (AMR) AF: 0.543 AC: 8300 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2001 AN: 3468

East Asian (EAS) AF: 0.331 AC: 1710 AN: 5168

South Asian (SAS) AF: 0.410 AC: 1970 AN: 4808

European-Finnish (FIN) AF: 0.743 AC: 7869 AN: 10588

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42375 AN: 67996

Other (OTH) AF: 0.474 AC: 1002 AN: 2114

Alfa AF: 0.573 Hom.: 116629

Bravo AF: 0.456

Asia WGS AF: 0.313 AC: 1089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.29
DANN	Benign	0.78
PhyloP100		-0.21

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1551398;

hg19: chr8-126540051;