rs2833522

Variant names:

• chr21-31807059-G-A
• rs2833522

Your query was ambiguous. Multiple possible variants found:

• chr21-31807059-G-A
• chr21-31807059-G-C

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 0.364 in 152,068 control chromosomes in the GnomAD database, including 10,292 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 0.36 (10292 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.443 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: 0.365 AC: 55415 AN: 151948 Hom.: 10290 Cov.: 33

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.364 AC: 55426 AN: 152068 Hom.: 10292 Cov.: 33 AF XY: 0.366 AC XY: 27196 AN XY: 74338

African (AFR) AF: 0.376 AC: 15585 AN: 41464

American (AMR) AF: 0.267 AC: 4081 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1039 AN: 3466

East Asian (EAS) AF: 0.458 AC: 2368 AN: 5168

South Asian (SAS) AF: 0.376 AC: 1812 AN: 4822

European-Finnish (FIN) AF: 0.432 AC: 4563 AN: 10574

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24905 AN: 67978

Other (OTH) AF: 0.344 AC: 727 AN: 2112

Alfa AF: 0.349 Hom.: 13335

Bravo AF: 0.349

Asia WGS AF: 0.409 AC: 1425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.53
DANN	Benign	0.36
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2833522; hg19: chr21-33179371;