chr21-16673913-A-G

Variant names:

• chr21-16673913-A-G
• rs2823962

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.588

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.755

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.453

Alfa AF: 0.417 Hom.: 23833

Bravo AF: 0.463

Asia WGS AF: 0.626 AC: 2177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2823962; hg19: chr21-18046232;