21-33395791-A-G

Variant names:

• chr21-33395791-A-G
• rs9976971

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 0.659 in 151,980 control chromosomes in the GnomAD database, including 34,565 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 0.66 (34565 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99996 AN: 151862 Hom.: 34509 Cov.: 30

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.659 AC: 100103 AN: 151980 Hom.: 34565 Cov.: 30 AF XY: 0.655 AC XY: 48681 AN XY: 74286

African (AFR) AF: 0.891 AC: 36971 AN: 41482

American (AMR) AF: 0.583 AC: 8891 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 2001 AN: 3472

East Asian (EAS) AF: 0.594 AC: 3053 AN: 5136

South Asian (SAS) AF: 0.651 AC: 3137 AN: 4816

European-Finnish (FIN) AF: 0.546 AC: 5756 AN: 10548

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38339 AN: 67954

Other (OTH) AF: 0.643 AC: 1357 AN: 2112

Alfa AF: 0.595 Hom.: 85719

Bravo AF: 0.670

Asia WGS AF: 0.671 AC: 2332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.61
DANN	Benign	0.76
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs9976971; hg19: chr21-34768097;