21-16673913-A-G

Variant names:

• chr21-16673913-A-G
• rs2823962

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 0.459 in 151,968 control chromosomes in the GnomAD database, including 17,091 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 0.46 (17091 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69778 AN: 151850 Hom.: 17086 Cov.: 31

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.459 AC: 69810 AN: 151968 Hom.: 17091 Cov.: 31 AF XY: 0.460 AC XY: 34193 AN XY: 74252

African (AFR) AF: 0.588 AC: 24360 AN: 41446

American (AMR) AF: 0.354 AC: 5405 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1637 AN: 3470

East Asian (EAS) AF: 0.755 AC: 3895 AN: 5156

South Asian (SAS) AF: 0.587 AC: 2828 AN: 4816

European-Finnish (FIN) AF: 0.328 AC: 3462 AN: 10554

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26523 AN: 67946

Other (OTH) AF: 0.453 AC: 957 AN: 2112

Alfa AF: 0.420 Hom.: 52889

Bravo AF: 0.463

Asia WGS AF: 0.626 AC: 2177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.85
PhyloP100		0.015

Splicing

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

Other links and lift over

dbSNP: rs2823962; hg19: chr21-18046232;