21-26835071-A-C

Variant names:

• chr21-26835071-A-C
• rs229040

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 0.333 in 151,988 control chromosomes in the GnomAD database, including 8,606 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 0.33 (8606 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 5 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 = 0.352 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: 0.333 AC: 50555 AN: 151870 Hom.: 8600 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.333 AC: 50587 AN: 151988 Hom.: 8606 Cov.: 32 AF XY: 0.331 AC XY: 24604 AN XY: 74310

African (AFR) AF: 0.331 AC: 13712 AN: 41426

American (AMR) AF: 0.317 AC: 4837 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 995 AN: 3460

East Asian (EAS) AF: 0.160 AC: 826 AN: 5166

South Asian (SAS) AF: 0.226 AC: 1088 AN: 4816

European-Finnish (FIN) AF: 0.374 AC: 3954 AN: 10580

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24180 AN: 67950

Other (OTH) AF: 0.297 AC: 626 AN: 2106

Alfa AF: 0.229 Hom.: 580

Bravo AF: 0.327

Asia WGS AF: 0.197 AC: 687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.32
PhyloP100		-0.019

Splicing

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

Other links and lift over

dbSNP: rs229040; hg19: chr21-28207390;