22-17731426-C-G

Variant names:

• chr22-17731426-C-G
• rs424708

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0306 AC: 1273 AN: 41542

American (AMR) AF: 0.103 AC: 1581 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0934 AC: 324 AN: 3468

East Asian (EAS) AF: 0.00774 AC: 40 AN: 5170

South Asian (SAS) AF: 0.0508 AC: 245 AN: 4820

European-Finnish (FIN) AF: 0.186 AC: 1971 AN: 10604

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11910 AN: 67990

Other (OTH) AF: 0.106 AC: 223 AN: 2112

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
PhyloP100		-4.5

Splicing

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

Other links and lift over

dbSNP: rs424708; hg19: chr22-18214192;