rs28913902

Variant names:

• chr4-99322742-G-GA
• rs28913902

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.83 (53034 hom., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 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: 0.834 AC: 126799 AN: 152030 Hom.: 52980 Cov.: 0

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.783

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.805

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.834 AC: 126905 AN: 152148 Hom.: 53034 Cov.: 0 AF XY: 0.834 AC XY: 62011 AN XY: 74358

African (AFR) AF: 0.891 AC: 36989 AN: 41536

American (AMR) AF: 0.837 AC: 12773 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.783 AC: 2718 AN: 3472

East Asian (EAS) AF: 0.923 AC: 4773 AN: 5170

South Asian (SAS) AF: 0.786 AC: 3780 AN: 4812

European-Finnish (FIN) AF: 0.805 AC: 8513 AN: 10570

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.802 AC: 54564 AN: 68000

Other (OTH) AF: 0.831 AC: 1757 AN: 2114

Alfa AF: 0.823 Hom.: 5521

Bravo AF: 0.839

Asia WGS AF: 0.825 AC: 2869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs28913902; hg19: chr4-100243899;