rs2048126

chr21-30682704-A-Gchr21-30682704-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.569

Alfa AF: 0.558 Hom.: 10734

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2048126; hg19: chr21-32055022;