rs2187226

Variant names:

• chr21-26731325-A-G
• rs2187226

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 0.864 in 152,114 control chromosomes in the GnomAD database, including 57,505 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 0.86 (57505 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888
• Publications: 5 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 = 0.96 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.864 AC: 131255 AN: 151996 Hom.: 57442 Cov.: 30

Gnomad AFR AF: 0.968

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.835

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

GnomAD4 genome AF: 0.864 AC: 131377 AN: 152114 Hom.: 57505 Cov.: 30 AF XY: 0.858 AC XY: 63757 AN XY: 74330

African (AFR) AF: 0.968 AC: 40186 AN: 41532

American (AMR) AF: 0.796 AC: 12177 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.837 AC: 2901 AN: 3468

East Asian (EAS) AF: 0.453 AC: 2323 AN: 5132

South Asian (SAS) AF: 0.816 AC: 3923 AN: 4810

European-Finnish (FIN) AF: 0.832 AC: 8799 AN: 10572

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.858 AC: 58370 AN: 67994

Other (OTH) AF: 0.837 AC: 1769 AN: 2114

Alfa AF: 0.854 Hom.: 103974

Bravo AF: 0.865

Asia WGS AF: 0.658 AC: 2287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.15
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs2187226; hg19: chr21-28103644;