chr21-26731325-A-G

Variant names:

• chr21-26731325-A-G
• rs2187226

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.968

Gnomad4 AMR AF: 0.796

Gnomad4 ASJ AF: 0.837

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.816

Gnomad4 FIN AF: 0.832

Gnomad4 NFE AF: 0.858

Gnomad4 OTH AF: 0.837

Alfa AF: 0.854 Hom.: 74786

Bravo AF: 0.865

Asia WGS AF: 0.658 AC: 2287 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2187226; hg19: chr21-28103644;