rs2099821

chr5-3223630-G-A

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 0.17 in 151,988 control chromosomes in the GnomAD database, including 2,322 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 0.17 (2322 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.239 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: 0.170 AC: 25794 AN: 151870 Hom.: 2324 Cov.: 30

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.170 AC: 25801 AN: 151988 Hom.: 2322 Cov.: 30 AF XY: 0.172 AC XY: 12743 AN XY: 74290

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.190

Alfa AF: 0.171 Hom.: 1021

Bravo AF: 0.168

Asia WGS AF: 0.185 AC: 642 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.3
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2099821; hg19: chr5-3223744;