rs2048126

Variant names:

• chr21-30682704-A-G
• rs2048126

Your query was ambiguous. Multiple possible variants found:

• chr21-30682704-A-G
• chr21-30682704-A-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 0.512 in 151,986 control chromosomes in the GnomAD database, including 20,692 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 0.51 (20692 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.601 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: 0.512 AC: 77709 AN: 151868 Hom.: 20676 Cov.: 31

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.512 AC: 77762 AN: 151986 Hom.: 20692 Cov.: 31 AF XY: 0.510 AC XY: 37871 AN XY: 74320

African (AFR) AF: 0.381 AC: 15771 AN: 41446

American (AMR) AF: 0.611 AC: 9331 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2139 AN: 3468

East Asian (EAS) AF: 0.310 AC: 1598 AN: 5160

South Asian (SAS) AF: 0.609 AC: 2936 AN: 4822

European-Finnish (FIN) AF: 0.489 AC: 5166 AN: 10554

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38862 AN: 67956

Other (OTH) AF: 0.569 AC: 1196 AN: 2102

Alfa AF: 0.558 Hom.: 12086

Bravo AF: 0.514

Asia WGS AF: 0.497 AC: 1730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.44
PhyloP100		-0.018

Splicing

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

Other links and lift over

dbSNP: rs2048126; hg19: chr21-32055022;