22-39326881-G-A

Variant names:

• chr22-39326881-G-A
• rs11704319

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.180 AC: 7424 AN: 41326

American (AMR) AF: 0.364 AC: 5475 AN: 15036

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 951 AN: 3464

East Asian (EAS) AF: 0.809 AC: 4122 AN: 5096

South Asian (SAS) AF: 0.416 AC: 2002 AN: 4808

European-Finnish (FIN) AF: 0.384 AC: 4053 AN: 10542

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.310 AC: 21040 AN: 67940

Other (OTH) AF: 0.323 AC: 676 AN: 2096

Alfa AF: 0.299 Hom.: 7900

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
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs11704319; hg19: chr22-39722886;