21-27821868-T-C

Variant names:

• chr21-27821868-T-C
• rs243687

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 0.594 in 152,098 control chromosomes in the GnomAD database, including 26,930 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 0.59 (26930 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.636 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: 0.594 AC: 90264 AN: 151980 Hom.: 26895 Cov.: 33

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.594 AC: 90360 AN: 152098 Hom.: 26930 Cov.: 33 AF XY: 0.588 AC XY: 43719 AN XY: 74354

African (AFR) AF: 0.642 AC: 26648 AN: 41494

American (AMR) AF: 0.623 AC: 9526 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.515 AC: 1788 AN: 3470

East Asian (EAS) AF: 0.579 AC: 2994 AN: 5172

South Asian (SAS) AF: 0.523 AC: 2525 AN: 4826

European-Finnish (FIN) AF: 0.481 AC: 5072 AN: 10554

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39885 AN: 67982

Other (OTH) AF: 0.564 AC: 1188 AN: 2108

Alfa AF: 0.594 Hom.: 4503

Bravo AF: 0.605

Asia WGS AF: 0.545 AC: 1892 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.72
DANN	Benign	0.67
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs243687; hg19: chr21-29194187;