8-125522429-A-G

Variant names:

• chr8-125522429-A-G
• rs921720
• ENST00000521991.2:n.281-258A>G

Variant summary

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

The ENST00000521991.2(TRIB1AL):​n.281-258A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 152,046 control chromosomes in the GnomAD database, including 21,159 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 0.49 (21159 hom., cov: 31)
• Consequence: TRIB1AL ENST00000521991.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• 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=-0.88).
• 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIB1AL	NR_186610.1		n.409-18481A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRIB1AL	ENST00000521991.2	TSL:2	n.281-258A>G		intron	N/A
	TRIB1AL	ENST00000522815.1	TSL:3	n.275-18481A>G		intron	N/A
	TRIB1AL	ENST00000772044.1		n.420-314A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73809 AN: 151928 Hom.: 21155 Cov.: 31

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.744

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: 0.485 AC: 73814 AN: 152046 Hom.: 21159 Cov.: 31 AF XY: 0.490 AC XY: 36397 AN XY: 74326

African (AFR) AF: 0.178 AC: 7396 AN: 41482

American (AMR) AF: 0.543 AC: 8298 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2005 AN: 3468

East Asian (EAS) AF: 0.396 AC: 2043 AN: 5154

South Asian (SAS) AF: 0.418 AC: 2015 AN: 4818

European-Finnish (FIN) AF: 0.744 AC: 7847 AN: 10554

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

European-Non Finnish (NFE) AF: 0.623 AC: 42367 AN: 67976

Other (OTH) AF: 0.474 AC: 1003 AN: 2114

Alfa AF: 0.557 Hom.: 70206

Bravo AF: 0.458

Asia WGS AF: 0.337 AC: 1173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.066
DANN	Benign	0.73
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs921720; hg19: chr8-126534671;