1-22348728-A-G

Variant names:

• chr1-22348728-A-G
• rs12137135

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;