1-22348728-A-G

Position:

• chr1-22348728-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 0.133 in 152,060 control chromosomes in the GnomAD database, including 1,726 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 0.13 (1726 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.22348728A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20200 AN: 151940 Hom.: 1726 Cov.: 30

Gnomad AFR AF: 0.0317

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.133 AC: 20208 AN: 152060 Hom.: 1726 Cov.: 30 AF XY: 0.139 AC XY: 10326 AN XY: 74318

Gnomad4 AFR AF: 0.0316

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.160

Alfa AF: 0.141 Hom.: 955

Bravo AF: 0.131

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.11
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12137135; hg19: chr1-22675221; COSMIC: COSV59931151;