rs2837253

Variant names:

• chr21-39849329-G-A
• rs2837253

Your query was ambiguous. Multiple possible variants found:

• chr21-39849329-G-A
• chr21-39849329-G-C
• chr21-39849329-G-T

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 0.267 in 152,034 control chromosomes in the GnomAD database, including 6,557 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 0.27 (6557 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40577 AN: 151916 Hom.: 6540 Cov.: 33

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.267 AC: 40617 AN: 152034 Hom.: 6557 Cov.: 33 AF XY: 0.274 AC XY: 20339 AN XY: 74316

African (AFR) AF: 0.103 AC: 4278 AN: 41512

American (AMR) AF: 0.422 AC: 6437 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1192 AN: 3470

East Asian (EAS) AF: 0.466 AC: 2399 AN: 5144

South Asian (SAS) AF: 0.362 AC: 1742 AN: 4808

European-Finnish (FIN) AF: 0.300 AC: 3170 AN: 10570

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.300 AC: 20405 AN: 67964

Other (OTH) AF: 0.275 AC: 580 AN: 2108

Alfa AF: 0.276 Hom.: 4264

Bravo AF: 0.272

Asia WGS AF: 0.384 AC: 1335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.56
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs2837253; hg19: chr21-41221256;