chr21-33316948-A-G

Position:

• chr21-33316948-A-G

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 0.779 in 152,122 control chromosomes in the GnomAD database, including 46,880 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 0.78 (46880 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.633

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.9 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: 0.779 AC: 118470 AN: 152004 Hom.: 46838 Cov.: 31

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.779 AC: 118566 AN: 152122 Hom.: 46880 Cov.: 31 AF XY: 0.780 AC XY: 57986 AN XY: 74376

Gnomad4 AFR AF: 0.908

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.789

Gnomad4 NFE AF: 0.723

Gnomad4 OTH AF: 0.765

Alfa AF: 0.743 Hom.: 19165

Bravo AF: 0.778

Asia WGS AF: 0.831 AC: 2890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2834188; hg19: chr21-34689253;