rs229038

Positions:

• chr21-26833110-C-G
• chr21-26833110-C-T
• chr21-26833110-C-A

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 0.895 in 152,260 control chromosomes in the GnomAD database, including 61,688 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 0.89 (61688 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.895 AC: 136123 AN: 152142 Hom.: 61629 Cov.: 33

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.959

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.895 AC: 136237 AN: 152260 Hom.: 61688 Cov.: 33 AF XY: 0.889 AC XY: 66153 AN XY: 74438

Gnomad4 AFR AF: 0.842

Gnomad4 AMR AF: 0.891

Gnomad4 ASJ AF: 0.925

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.883

Gnomad4 FIN AF: 0.893

Gnomad4 NFE AF: 0.959

Gnomad4 OTH AF: 0.874

Alfa AF: 0.932 Hom.: 8223

Bravo AF: 0.892

Asia WGS AF: 0.711 AC: 2472 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	0.86
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs229038; hg19: chr21-28205429;