8-109085959-A-G

Variant names:

• chr8-109085959-A-G
• rs3110037

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 0.625 in 151,876 control chromosomes in the GnomAD database, including 29,861 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 0.63 (29861 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.175
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.709 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: 0.625 AC: 94873 AN: 151756 Hom.: 29829 Cov.: 30

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.625 AC: 94969 AN: 151876 Hom.: 29861 Cov.: 30 AF XY: 0.630 AC XY: 46723 AN XY: 74202

African (AFR) AF: 0.642 AC: 26579 AN: 41402

American (AMR) AF: 0.719 AC: 10981 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1699 AN: 3466

East Asian (EAS) AF: 0.569 AC: 2922 AN: 5132

South Asian (SAS) AF: 0.730 AC: 3492 AN: 4786

European-Finnish (FIN) AF: 0.606 AC: 6400 AN: 10558

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.600 AC: 40784 AN: 67948

Other (OTH) AF: 0.645 AC: 1364 AN: 2114

Alfa AF: 0.491 Hom.: 1244

Bravo AF: 0.661

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.019
DANN	Benign	0.38
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs3110037; hg19: chr8-110098188;