rs5766424

Variant names:

• chr22-45106652-G-A
• rs5766424

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 0.505 in 152,090 control chromosomes in the GnomAD database, including 20,014 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 0.50 (20014 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

ACMG classification

Verdict is Benign. Variant got -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 = 0.853 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: 0.505 AC: 76686 AN: 151972 Hom.: 20004 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.565

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.505 AC: 76733 AN: 152090 Hom.: 20014 Cov.: 32 AF XY: 0.515 AC XY: 38308 AN XY: 74374

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.603

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.874

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.565

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.527

Alfa AF: 0.479 Hom.: 24718

Bravo AF: 0.506

Asia WGS AF: 0.681 AC: 2371 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	0.49
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5766424; hg19: chr22-45502533;