chr22-45452390-C-T

Variant names:

• chr22-45452390-C-T
• rs16994023

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 0.0527 in 152,300 control chromosomes in the GnomAD database, including 540 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 0.053 (540 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 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: 0.0526 AC: 8003 AN: 152182 Hom.: 535 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0248

Gnomad ASJ AF: 0.0256

Gnomad EAS AF: 0.0585

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.00188

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.00735

Gnomad OTH AF: 0.0392

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

GnomAD4 genome AF: 0.0527 AC: 8027 AN: 152300 Hom.: 540 Cov.: 32 AF XY: 0.0526 AC XY: 3920 AN XY: 74468

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.0248

Gnomad4 ASJ AF: 0.0256

Gnomad4 EAS AF: 0.0584

Gnomad4 SAS AF: 0.0379

Gnomad4 FIN AF: 0.00188

Gnomad4 NFE AF: 0.00735

Gnomad4 OTH AF: 0.0440

Alfa AF: 0.0170 Hom.: 95

Bravo AF: 0.0579

Asia WGS AF: 0.0810 AC: 281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.97
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16994023; hg19: chr22-45848271;