rs5750326

Variant names:

• chr22-36880243-C-A
• rs5750326

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 0.45 in 150,838 control chromosomes in the GnomAD database, including 16,187 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 0.45 (16187 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.569 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: 0.450 AC: 67870 AN: 150728 Hom.: 16177 Cov.: 29

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.450 AC: 67908 AN: 150838 Hom.: 16187 Cov.: 29 AF XY: 0.457 AC XY: 33642 AN XY: 73646

African (AFR) AF: 0.280 AC: 11446 AN: 40868

American (AMR) AF: 0.502 AC: 7614 AN: 15158

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1644 AN: 3458

East Asian (EAS) AF: 0.586 AC: 2999 AN: 5116

South Asian (SAS) AF: 0.481 AC: 2298 AN: 4774

European-Finnish (FIN) AF: 0.597 AC: 6195 AN: 10382

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.504 AC: 34197 AN: 67786

Other (OTH) AF: 0.458 AC: 961 AN: 2098

Alfa AF: 0.484 Hom.: 77663

Bravo AF: 0.432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.97
DANN	Benign	0.61
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs5750326; hg19: chr22-37276285;