22-39326881-G-A

Position:

• chr22-39326881-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 0.305 in 151,510 control chromosomes in the GnomAD database, including 8,304 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 0.30 (8304 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28

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 (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46107 AN: 151396 Hom.: 8295 Cov.: 31

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.305 AC: 46141 AN: 151510 Hom.: 8304 Cov.: 31 AF XY: 0.314 AC XY: 23275 AN XY: 74034

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.809

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.323

Alfa AF: 0.308 Hom.: 5611

Bravo AF: 0.302

Asia WGS AF: 0.567 AC: 1966 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	11
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11704319; hg19: chr22-39722886;