21-27455371-G-A

Variant names:

• chr21-27455371-G-A
• rs242326

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 0.919 in 152,220 control chromosomes in the GnomAD database, including 64,332 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 0.92 (64332 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.559
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.918 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: 0.919 AC: 139789 AN: 152102 Hom.: 64288 Cov.: 31

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.989

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.852

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.967

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.924

Gnomad OTH AF: 0.908

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

GnomAD4 genome AF: 0.919 AC: 139893 AN: 152220 Hom.: 64332 Cov.: 31 AF XY: 0.920 AC XY: 68491 AN XY: 74428

African (AFR) AF: 0.914 AC: 37952 AN: 41524

American (AMR) AF: 0.897 AC: 13706 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.852 AC: 2957 AN: 3472

East Asian (EAS) AF: 0.904 AC: 4676 AN: 5174

South Asian (SAS) AF: 0.911 AC: 4390 AN: 4818

European-Finnish (FIN) AF: 0.967 AC: 10269 AN: 10616

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.924 AC: 62874 AN: 68014

Other (OTH) AF: 0.903 AC: 1911 AN: 2116

Alfa AF: 0.916 Hom.: 114488

Bravo AF: 0.914

Asia WGS AF: 0.888 AC: 3088 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.5
DANN	Benign	0.64
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs242326; hg19: chr21-28827690;