22-17731426-C-G

Variant names:

• chr22-17731426-C-G
• rs424708

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 0.117 in 152,210 control chromosomes in the GnomAD database, including 1,468 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 0.12 (1468 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.173 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: 0.117 AC: 17735 AN: 152092 Hom.: 1468 Cov.: 31

Gnomad AFR AF: 0.0307

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0934

Gnomad EAS AF: 0.00753

Gnomad SAS AF: 0.0504

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.117 AC: 17739 AN: 152210 Hom.: 1468 Cov.: 31 AF XY: 0.115 AC XY: 8551 AN XY: 74422

Gnomad4 AFR AF: 0.0306

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0934

Gnomad4 EAS AF: 0.00774

Gnomad4 SAS AF: 0.0508

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0693 Hom.: 134

Bravo AF: 0.107

Asia WGS AF: 0.0370 AC: 130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs424708; hg19: chr22-18214192;