rs424708

chr22-17731426-C-Gchr22-17731426-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;