rs5999839

chr22-35497664-A-G

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 0.068 in 152,182 control chromosomes in the GnomAD database, including 752 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 0.068 (752 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 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: 0.0679 AC: 10324 AN: 152064 Hom.: 750 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.0463

Gnomad AMR AF: 0.0490

Gnomad ASJ AF: 0.0565

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0124

Gnomad FIN AF: 0.0138

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0256

Gnomad OTH AF: 0.0522

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

GnomAD4 genome AF: 0.0680 AC: 10346 AN: 152182 Hom.: 752 Cov.: 32 AF XY: 0.0679 AC XY: 5053 AN XY: 74416

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.0489

Gnomad4 ASJ AF: 0.0565

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0125

Gnomad4 FIN AF: 0.0138

Gnomad4 NFE AF: 0.0256

Gnomad4 OTH AF: 0.0517

Alfa AF: 0.0529 Hom.: 64

Bravo AF: 0.0765

Asia WGS AF: 0.0160 AC: 58 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	6.7
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5999839; hg19: chr22-35893711;