rs3912099

Variant names:

• chr3-162434210-G-A
• rs3912099

Your query was ambiguous. Multiple possible variants found:

• chr3-162434210-G-A
• chr3-162434210-G-C
• chr3-162434210-G-T

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 0.892 in 152,040 control chromosomes in the GnomAD database, including 60,723 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 0.89 (60723 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.967 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: 0.892 AC: 135465 AN: 151922 Hom.: 60668 Cov.: 31

Gnomad AFR AF: 0.969

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.929

Gnomad EAS AF: 0.990

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.856

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.900

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

GnomAD4 genome AF: 0.892 AC: 135579 AN: 152040 Hom.: 60723 Cov.: 31 AF XY: 0.894 AC XY: 66404 AN XY: 74284

African (AFR) AF: 0.969 AC: 40236 AN: 41514

American (AMR) AF: 0.917 AC: 13979 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.929 AC: 3225 AN: 3470

East Asian (EAS) AF: 0.989 AC: 5086 AN: 5140

South Asian (SAS) AF: 0.880 AC: 4243 AN: 4820

European-Finnish (FIN) AF: 0.856 AC: 9060 AN: 10580

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.837 AC: 56846 AN: 67954

Other (OTH) AF: 0.901 AC: 1901 AN: 2110

Alfa AF: 0.872 Hom.: 10677

Bravo AF: 0.900

Asia WGS AF: 0.940 AC: 3265 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.1
DANN	Benign	0.48
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs3912099; hg19: chr3-162151998;