rs2403104

Variant names:

• chr8-85319199-G-T
• rs2403104

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 0.762 in 152,088 control chromosomes in the GnomAD database, including 45,294 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 (45294 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.652
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.913 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: 0.762 AC: 115770 AN: 151970 Hom.: 45233 Cov.: 32

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.826

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.762 AC: 115886 AN: 152088 Hom.: 45294 Cov.: 32 AF XY: 0.761 AC XY: 56573 AN XY: 74346

African (AFR) AF: 0.921 AC: 38218 AN: 41510

American (AMR) AF: 0.629 AC: 9605 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2346 AN: 3470

East Asian (EAS) AF: 0.467 AC: 2413 AN: 5172

South Asian (SAS) AF: 0.629 AC: 3031 AN: 4816

European-Finnish (FIN) AF: 0.826 AC: 8731 AN: 10566

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.724 AC: 49241 AN: 67970

Other (OTH) AF: 0.743 AC: 1563 AN: 2104

Alfa AF: 0.771 Hom.: 6944

Bravo AF: 0.751

Asia WGS AF: 0.584 AC: 2028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.027
DANN	Benign	0.46
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs2403104; hg19: chr8-86231428;