21-46606442-G-A

Variant names:

• chr21-46606442-G-A
• rs3788266

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 0.496 in 152,206 control chromosomes in the GnomAD database, including 19,008 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 0.50 (19008 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.937
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.536 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: 0.496 AC: 75496 AN: 152088 Hom.: 18993 Cov.: 34

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.496 AC: 75561 AN: 152206 Hom.: 19008 Cov.: 34 AF XY: 0.500 AC XY: 37227 AN XY: 74412

African (AFR) AF: 0.542 AC: 22498 AN: 41520

American (AMR) AF: 0.488 AC: 7463 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1728 AN: 3472

East Asian (EAS) AF: 0.260 AC: 1345 AN: 5174

South Asian (SAS) AF: 0.373 AC: 1797 AN: 4822

European-Finnish (FIN) AF: 0.573 AC: 6075 AN: 10606

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.485 AC: 32966 AN: 68000

Other (OTH) AF: 0.504 AC: 1066 AN: 2114

Alfa AF: 0.493 Hom.: 11491

Bravo AF: 0.492

Asia WGS AF: 0.325 AC: 1131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.19
DANN	Benign	0.45
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs3788266; hg19: chr21-48026355;