3-83498284-A-G

Variant names:

• chr3-83498284-A-G
• rs8180101

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 0.846 in 152,098 control chromosomes in the GnomAD database, including 54,552 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 0.85 (54552 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.845 AC: 128497 AN: 151980 Hom.: 54502 Cov.: 31

Gnomad AFR AF: 0.772

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.892

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.871

Gnomad FIN AF: 0.856

Gnomad MID AF: 0.876

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.855

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

GnomAD4 genome AF: 0.846 AC: 128606 AN: 152098 Hom.: 54552 Cov.: 31 AF XY: 0.849 AC XY: 63080 AN XY: 74320

African (AFR) AF: 0.772 AC: 32044 AN: 41484

American (AMR) AF: 0.892 AC: 13618 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.870 AC: 3019 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5145 AN: 5154

South Asian (SAS) AF: 0.871 AC: 4201 AN: 4822

European-Finnish (FIN) AF: 0.856 AC: 9056 AN: 10574

Middle Eastern (MID) AF: 0.873 AC: 255 AN: 292

European-Non Finnish (NFE) AF: 0.863 AC: 58703 AN: 68004

Other (OTH) AF: 0.857 AC: 1811 AN: 2112

Alfa AF: 0.860 Hom.: 24304

Bravo AF: 0.845

Asia WGS AF: 0.935 AC: 3249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.026
DANN	Benign	0.33
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs8180101; hg19: chr3-83547435;