21-30185998-G-A

Variant names:

• chr21-30185998-G-A
• rs651084

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 0.735 in 152,124 control chromosomes in the GnomAD database, including 42,183 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 0.74 (42183 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.512
• Publications: 5 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 (SAS) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111765 AN: 152006 Hom.: 42172 Cov.: 32

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.823

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.735 AC: 111816 AN: 152124 Hom.: 42183 Cov.: 32 AF XY: 0.738 AC XY: 54892 AN XY: 74376

African (AFR) AF: 0.579 AC: 23997 AN: 41460

American (AMR) AF: 0.674 AC: 10286 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.826 AC: 2867 AN: 3472

East Asian (EAS) AF: 0.484 AC: 2495 AN: 5160

South Asian (SAS) AF: 0.868 AC: 4183 AN: 4818

European-Finnish (FIN) AF: 0.882 AC: 9354 AN: 10608

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.825 AC: 56081 AN: 68012

Other (OTH) AF: 0.739 AC: 1563 AN: 2116

Alfa AF: 0.786 Hom.: 88304

Bravo AF: 0.701

Asia WGS AF: 0.689 AC: 2394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.33
DANN	Benign	0.57
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs651084; hg19: chr21-31558316;