22-49957323-G-A

Variant names:

• chr22-49957323-G-A
• rs28372448

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 0.073 in 152,092 control chromosomes in the GnomAD database, including 498 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 0.073 (498 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0729 AC: 11084 AN: 151974 Hom.: 494 Cov.: 33

Gnomad AFR AF: 0.0854

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0382

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.0786

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0600

Gnomad OTH AF: 0.0589

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

GnomAD4 genome AF: 0.0730 AC: 11105 AN: 152092 Hom.: 498 Cov.: 33 AF XY: 0.0760 AC XY: 5651 AN XY: 74374

African (AFR) AF: 0.0856 AC: 3549 AN: 41476

American (AMR) AF: 0.0382 AC: 584 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0372 AC: 129 AN: 3464

East Asian (EAS) AF: 0.143 AC: 734 AN: 5150

South Asian (SAS) AF: 0.0783 AC: 378 AN: 4828

European-Finnish (FIN) AF: 0.141 AC: 1493 AN: 10614

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0601 AC: 4083 AN: 67954

Other (OTH) AF: 0.0601 AC: 127 AN: 2112

Alfa AF: 0.0626 Hom.: 1174

Bravo AF: 0.0645

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.033
DANN	Benign	0.52
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs28372448; hg19: chr22-50350971;