chr21-33316948-A-G

Variant names:

• chr21-33316948-A-G
• rs2834188

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 0.779 in 152,122 control chromosomes in the GnomAD database, including 46,880 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 0.78 (46880 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.633
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.9 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: 0.779 AC: 118470 AN: 152004 Hom.: 46838 Cov.: 31

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.779 AC: 118566 AN: 152122 Hom.: 46880 Cov.: 31 AF XY: 0.780 AC XY: 57986 AN XY: 74376

African (AFR) AF: 0.908 AC: 37673 AN: 41508

American (AMR) AF: 0.707 AC: 10800 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2177 AN: 3472

East Asian (EAS) AF: 0.753 AC: 3885 AN: 5162

South Asian (SAS) AF: 0.824 AC: 3975 AN: 4824

European-Finnish (FIN) AF: 0.789 AC: 8345 AN: 10570

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.723 AC: 49167 AN: 68002

Other (OTH) AF: 0.765 AC: 1615 AN: 2110

Alfa AF: 0.735 Hom.: 78740

Bravo AF: 0.778

Asia WGS AF: 0.831 AC: 2890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.60
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2834188; hg19: chr21-34689253;