8-125511281-C-T

Variant names:

• chr8-125511281-C-T
• rs4360309
• ENST00000521991.2:n.281-11406C>T

Variant summary

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

The ENST00000521991.2(TRIB1AL):​n.281-11406C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 152,142 control chromosomes in the GnomAD database, including 36,814 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 0.67 (36814 hom., cov: 33)
• Consequence: TRIB1AL ENST00000521991.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348
• Publications: 20 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.968 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRIB1AL	NR_186610.1	n.409-29629C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRIB1AL	ENST00000521991.2	n.281-11406C>T		intron_variant	Intron 1 of 2	2
TRIB1AL	ENST00000522815.1	n.275-29629C>T		intron_variant	Intron 2 of 3	3
TRIB1AL	ENST00000772044.1	n.72-1765C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101592 AN: 152024 Hom.: 36740 Cov.: 33

Gnomad AFR AF: 0.910

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.669 AC: 101729 AN: 152142 Hom.: 36814 Cov.: 33 AF XY: 0.675 AC XY: 50172 AN XY: 74364

African (AFR) AF: 0.911 AC: 37830 AN: 41542

American (AMR) AF: 0.733 AC: 11197 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2220 AN: 3470

East Asian (EAS) AF: 0.991 AC: 5137 AN: 5184

South Asian (SAS) AF: 0.821 AC: 3957 AN: 4822

European-Finnish (FIN) AF: 0.495 AC: 5233 AN: 10564

Middle Eastern (MID) AF: 0.664 AC: 194 AN: 292

European-Non Finnish (NFE) AF: 0.503 AC: 34153 AN: 67960

Other (OTH) AF: 0.654 AC: 1382 AN: 2112

Alfa AF: 0.565 Hom.: 66397

Bravo AF: 0.694

Asia WGS AF: 0.908 AC: 3157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.55
DANN	Benign	0.36
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs4360309; hg19: chr8-126523523;