chr8-125469233-A-T

Position:

• chr8-125469233-A-T

Variant summary

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

The NR_186610.1(TRIB1AL):​n.229+2200A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.688 in 152,052 control chromosomes in the GnomAD database, including 36,025 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 0.69 (36025 hom., cov: 32)
• Consequence: TRIB1AL NR_186610.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.788

Genes affected

ENSG00000253111 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.754 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIB1AL	NR_186610.1	n.229+2200A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000253111	ENST00000522815.1	n.95+2200A>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.688 AC: 104538 AN: 151934 Hom.: 35986 Cov.: 32

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.688 AC: 104631 AN: 152052 Hom.: 36025 Cov.: 32 AF XY: 0.689 AC XY: 51224 AN XY: 74326

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.577

Gnomad4 EAS AF: 0.696

Gnomad4 SAS AF: 0.774

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.664

Alfa AF: 0.695 Hom.: 4545

Bravo AF: 0.685

Asia WGS AF: 0.746 AC: 2594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.6
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2980879; hg19: chr8-126481475;