22-27483209-C-T

Position:

• chr22-27483209-C-T

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 0.598 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.27483209C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.635

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.509

Gnomad4 FIN AF: 0.838

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.616

Alfa AF: 0.714 Hom.: 58222

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs926837; hg19: chr22-27879170;