chr21-20512990-A-T

Variant names:

• chr21-20512990-A-T
• rs2826340

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 0.177 in 152,114 control chromosomes in the GnomAD database, including 2,445 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 0.18 (2445 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.48
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 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: 0.177 AC: 26861 AN: 151996 Hom.: 2440 Cov.: 31

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.0681

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.177 AC: 26878 AN: 152114 Hom.: 2445 Cov.: 31 AF XY: 0.176 AC XY: 13121 AN XY: 74360

African (AFR) AF: 0.200 AC: 8310 AN: 41490

American (AMR) AF: 0.173 AC: 2640 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 368 AN: 3472

East Asian (EAS) AF: 0.163 AC: 846 AN: 5178

South Asian (SAS) AF: 0.168 AC: 811 AN: 4828

European-Finnish (FIN) AF: 0.181 AC: 1910 AN: 10558

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11520 AN: 67986

Other (OTH) AF: 0.176 AC: 371 AN: 2112

Alfa AF: 0.180 Hom.: 295

Bravo AF: 0.175

Asia WGS AF: 0.175 AC: 609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.9
DANN	Benign	0.70
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs2826340; hg19: chr21-21885302;