rs5750326

chr22-36880243-C-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 0.45 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.502

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.504

Gnomad4 OTH AF: 0.458

Alfa AF: 0.490 Hom.: 37698

Bravo AF: 0.432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.97
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5750326; hg19: chr22-37276285;