rs12172263

Variant names:

• chr22-48442095-G-A
• rs12172263

Your query was ambiguous. Multiple possible variants found:

• chr22-48442095-G-A
• chr22-48442095-G-T

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 152,018 control chromosomes in the GnomAD database, including 1,210 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 (1210 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.149 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: 17724 AN: 151900 Hom.: 1210 Cov.: 31

Gnomad AFR AF: 0.0454

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0475

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.117 AC: 17724 AN: 152018 Hom.: 1210 Cov.: 31 AF XY: 0.120 AC XY: 8916 AN XY: 74298

African (AFR) AF: 0.0455 AC: 1887 AN: 41504

American (AMR) AF: 0.126 AC: 1922 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 352 AN: 3470

East Asian (EAS) AF: 0.0466 AC: 241 AN: 5170

South Asian (SAS) AF: 0.121 AC: 584 AN: 4828

European-Finnish (FIN) AF: 0.189 AC: 1997 AN: 10554

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10303 AN: 67914

Other (OTH) AF: 0.123 AC: 258 AN: 2106

Alfa AF: 0.141 Hom.: 3519

Bravo AF: 0.108

Asia WGS AF: 0.0720 AC: 251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.8
DANN	Benign	0.86
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs12172263; hg19: chr22-48837907;