21-16671032-A-G

Variant names:

• chr21-16671032-A-G
• rs2823953

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 0.481 in 151,716 control chromosomes in the GnomAD database, including 19,083 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 0.48 (19083 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 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: 0.481 AC: 72912 AN: 151598 Hom.: 19063 Cov.: 31

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.481 AC: 72967 AN: 151716 Hom.: 19083 Cov.: 31 AF XY: 0.481 AC XY: 35678 AN XY: 74144

African (AFR) AF: 0.658 AC: 27236 AN: 41364

American (AMR) AF: 0.363 AC: 5536 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1630 AN: 3462

East Asian (EAS) AF: 0.757 AC: 3905 AN: 5160

South Asian (SAS) AF: 0.598 AC: 2881 AN: 4816

European-Finnish (FIN) AF: 0.328 AC: 3454 AN: 10544

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.392 AC: 26607 AN: 67796

Other (OTH) AF: 0.462 AC: 973 AN: 2106

Alfa AF: 0.429 Hom.: 4009

Bravo AF: 0.487

Asia WGS AF: 0.641 AC: 2219 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.77
DANN	Benign	0.72
PhyloP100		-0.068

Splicing

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

Other links and lift over

dbSNP: rs2823953; hg19: chr21-18043351;