rs2742624

Positions:

• chr22-45280797-A-G

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 0.548 in 151,950 control chromosomes in the GnomAD database, including 26,195 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 0.55 (26195 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.667

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.45280797A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.549 AC: 83322 AN: 151832 Hom.: 26207 Cov.: 31

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.807

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.729

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.548 AC: 83322 AN: 151950 Hom.: 26195 Cov.: 31 AF XY: 0.549 AC XY: 40722 AN XY: 74240

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.615

Gnomad4 ASJ AF: 0.729

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.567

Alfa AF: 0.634 Hom.: 7709

Bravo AF: 0.530

Asia WGS AF: 0.462 AC: 1610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.3
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2742624; hg19: chr22-45676678;