rs2825699

Positions:

• chr21-19639917-A-C

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 0.204 in 151,654 control chromosomes in the GnomAD database, including 3,301 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 0.20 (3301 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.781

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30990 AN: 151540 Hom.: 3300 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.204 AC: 31012 AN: 151654 Hom.: 3301 Cov.: 32 AF XY: 0.207 AC XY: 15312 AN XY: 74122

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.210

Alfa AF: 0.193 Hom.: 2607

Bravo AF: 0.205

Asia WGS AF: 0.253 AC: 875 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.9
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2825699; hg19: chr21-21012231;