rs6987702

Variant names:

• chr8-125492484-T-C
• rs6987702
• ENST00000521991.2:n.280+5525T>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+5525T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 152,002 control chromosomes in the GnomAD database, including 16,906 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 0.43 (16906 hom., cov: 31)
• Consequence: TRIB1AL ENST00000521991.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.248
• Publications: 36 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.707 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+19170T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIB1AL	ENST00000521991.2	TSL:2	n.280+5525T>C		intron	N/A
	TRIB1AL	ENST00000522815.1	TSL:3	n.274+19170T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65161 AN: 151884 Hom.: 16873 Cov.: 31

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.429 AC: 65251 AN: 152002 Hom.: 16906 Cov.: 31 AF XY: 0.434 AC XY: 32221 AN XY: 74298

African (AFR) AF: 0.714 AC: 29582 AN: 41420

American (AMR) AF: 0.449 AC: 6860 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 717 AN: 3466

East Asian (EAS) AF: 0.562 AC: 2910 AN: 5174

South Asian (SAS) AF: 0.496 AC: 2388 AN: 4818

European-Finnish (FIN) AF: 0.319 AC: 3370 AN: 10550

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18453 AN: 67980

Other (OTH) AF: 0.360 AC: 759 AN: 2106

Alfa AF: 0.335 Hom.: 20901

Bravo AF: 0.449

Asia WGS AF: 0.526 AC: 1824 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.1
DANN	Benign	0.84
PhyloP100		-0.25

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: rs6987702;

hg19: chr8-126504726;