8-125472284-T-G

Position:

• chr8-125472284-T-G

Variant summary

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

The ENST00000522815.1(ENSG00000253111):​n.96-852T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,230 control chromosomes in the GnomAD database, including 44,700 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 0.76 (44700 hom., cov: 33)
• Consequence: ENSG00000253111 ENST00000522815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

Genes affected

ENSG00000253111 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TRIB1AL	NR_186610.1	n.230-852T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000253111	ENST00000522815.1	n.96-852T>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115655 AN: 152112 Hom.: 44636 Cov.: 33

Gnomad AFR AF: 0.907

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.761 AC: 115778 AN: 152230 Hom.: 44700 Cov.: 33 AF XY: 0.760 AC XY: 56592 AN XY: 74420

Gnomad4 AFR AF: 0.907

Gnomad4 AMR AF: 0.739

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.786

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.712

Alfa AF: 0.691 Hom.: 42767

Bravo AF: 0.765

Asia WGS AF: 0.761 AC: 2648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.9
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2954026; hg19: chr8-126484526;