rs2742624

Variant names:

• chr22-45280797-A-G
• rs2742624

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.667

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;