22-16945511-C-T

Variant names:

• chr22-16945511-C-T
• rs5748755

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 0.803 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.926 AC: 38416 AN: 41492

American (AMR) AF: 0.839 AC: 12812 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.780 AC: 2707 AN: 3472

East Asian (EAS) AF: 0.850 AC: 4398 AN: 5174

South Asian (SAS) AF: 0.724 AC: 3487 AN: 4814

European-Finnish (FIN) AF: 0.744 AC: 7779 AN: 10452

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.733 AC: 49804 AN: 67928

Other (OTH) AF: 0.805 AC: 1697 AN: 2108

Alfa AF: 0.738 Hom.: 18360

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs5748755; hg19: chr22-17426401;