22-27483209-C-T

Variant names:

• chr22-27483209-C-T
• rs926837

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 0.598 in 151,976 control chromosomes in the GnomAD database, including 30,404 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 0.60 (30404 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.753 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: 0.598 AC: 90825 AN: 151858 Hom.: 30406 Cov.: 31

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.598 AC: 90832 AN: 151976 Hom.: 30404 Cov.: 31 AF XY: 0.599 AC XY: 44526 AN XY: 74278

African (AFR) AF: 0.297 AC: 12310 AN: 41424

American (AMR) AF: 0.579 AC: 8831 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2204 AN: 3470

East Asian (EAS) AF: 0.453 AC: 2336 AN: 5156

South Asian (SAS) AF: 0.509 AC: 2448 AN: 4812

European-Finnish (FIN) AF: 0.838 AC: 8869 AN: 10580

Middle Eastern (MID) AF: 0.558 AC: 163 AN: 292

European-Non Finnish (NFE) AF: 0.759 AC: 51554 AN: 67962

Other (OTH) AF: 0.616 AC: 1298 AN: 2108

Alfa AF: 0.696 Hom.: 75586

Bravo AF: 0.565

Asia WGS AF: 0.488 AC: 1696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.49
DANN	Benign	0.63
PhyloP100		-0.066

Splicing

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

Other links and lift over

dbSNP: rs926837; hg19: chr22-27879170;