8-109073589-G-T

Variant names:

• chr8-109073589-G-T
• rs4506180

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.751 AC: 31166 AN: 41482

American (AMR) AF: 0.612 AC: 9355 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1367 AN: 3468

East Asian (EAS) AF: 0.558 AC: 2868 AN: 5144

South Asian (SAS) AF: 0.644 AC: 3107 AN: 4824

European-Finnish (FIN) AF: 0.537 AC: 5670 AN: 10556

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34505 AN: 67970

Other (OTH) AF: 0.562 AC: 1186 AN: 2110

Alfa AF: 0.529 Hom.: 86857

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
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs4506180; hg19: chr8-110085818;