chr8-125483576-C-T

Position:

• chr8-125483576-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000522815.1(TRIB1AL):​n.274+10262C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 151,842 control chromosomes in the GnomAD database, including 11,433 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 0.38 (11433 hom., cov: 31)
• Consequence: TRIB1AL ENST00000522815.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TRIB1AL	ENST00000522815.1	n.274+10262C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57666 AN: 151724 Hom.: 11423 Cov.: 31

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.342

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.380 AC: 57714 AN: 151842 Hom.: 11433 Cov.: 31 AF XY: 0.372 AC XY: 27608 AN XY: 74220

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.342

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.367

Alfa AF: 0.423 Hom.: 27851

Bravo AF: 0.371

Asia WGS AF: 0.204 AC: 713 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.82
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10808546; hg19: chr8-126495818;