8-109073589-G-T

Position:

• chr8-109073589-G-T

Variant summary

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

The variant allele was found at a frequency of 0.591 in 152,040 control chromosomes in the GnomAD database, including 27,654 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 0.59 (27654 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89758 AN: 151922 Hom.: 27615 Cov.: 33

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.591 AC: 89864 AN: 152040 Hom.: 27654 Cov.: 33 AF XY: 0.593 AC XY: 44046 AN XY: 74292

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.562

Alfa AF: 0.514 Hom.: 33553

Bravo AF: 0.600

Asia WGS AF: 0.621 AC: 2162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.8
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4506180; hg19: chr8-110085818;