chr8-125492484-T-C

Position:

• chr8-125492484-T-C

Variant summary

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

The ENST00000521991.2(ENSG00000253111):​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: ENSG00000253111 ENST00000521991.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.248

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 (AFR) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIB1AL	NR_186610.1	n.408+19170T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000253111	ENST00000521991.2	n.280+5525T>C		intron_variant		2
ENSG00000253111	ENST00000522815.1	n.274+19170T>C		intron_variant		3

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

Gnomad4 AFR AF: 0.714

Gnomad4 AMR AF: 0.449

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.319

Gnomad4 NFE AF: 0.271

Gnomad4 OTH AF: 0.360

Alfa AF: 0.306 Hom.: 3972

Bravo AF: 0.449

Asia WGS AF: 0.526 AC: 1824 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6987702; hg19: chr8-126504726;