22-16945511-C-T

Position:

• chr22-16945511-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 0.803 in 151,918 control chromosomes in the GnomAD database, including 49,452 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 0.80 (49452 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.16945511C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.803 AC: 121878 AN: 151800 Hom.: 49400 Cov.: 31

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.806

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

GnomAD4 genome AF: 0.803 AC: 121986 AN: 151918 Hom.: 49452 Cov.: 31 AF XY: 0.802 AC XY: 59592 AN XY: 74262

Gnomad4 AFR AF: 0.926

Gnomad4 AMR AF: 0.839

Gnomad4 ASJ AF: 0.780

Gnomad4 EAS AF: 0.850

Gnomad4 SAS AF: 0.724

Gnomad4 FIN AF: 0.744

Gnomad4 NFE AF: 0.733

Gnomad4 OTH AF: 0.805

Alfa AF: 0.738 Hom.: 16251

Bravo AF: 0.819

Asia WGS AF: 0.775 AC: 2692 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.4
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5748755; hg19: chr22-17426401;