rs2823954

Variant names:

• chr21-16671283-A-C
• rs2823954

Your query was ambiguous. Multiple possible variants found:

• chr21-16671283-A-C
• chr21-16671283-A-G
• chr21-16671283-A-T

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 0.458 in 151,862 control chromosomes in the GnomAD database, including 16,920 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 (16920 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.642 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: 0.459 AC: 69586 AN: 151744 Hom.: 16915 Cov.: 32

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.458 AC: 69616 AN: 151862 Hom.: 16920 Cov.: 32 AF XY: 0.459 AC XY: 34096 AN XY: 74244

African (AFR) AF: 0.593 AC: 24572 AN: 41440

American (AMR) AF: 0.355 AC: 5425 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1632 AN: 3462

East Asian (EAS) AF: 0.661 AC: 3413 AN: 5166

South Asian (SAS) AF: 0.598 AC: 2882 AN: 4816

European-Finnish (FIN) AF: 0.329 AC: 3471 AN: 10552

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26521 AN: 67840

Other (OTH) AF: 0.451 AC: 953 AN: 2112

Alfa AF: 0.310 Hom.: 856

Bravo AF: 0.461

Asia WGS AF: 0.596 AC: 2067 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.62
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs2823954; hg19: chr21-18043602;