rs12485068

Positions:

• chr22-23892747-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 0.198 in 152,018 control chromosomes in the GnomAD database, including 3,126 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 0.20 (3126 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.662

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30028 AN: 151896 Hom.: 3116 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.176

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.198 AC: 30069 AN: 152018 Hom.: 3126 Cov.: 32 AF XY: 0.203 AC XY: 15048 AN XY: 74310

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.236

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.178

Alfa AF: 0.195 Hom.: 399

Bravo AF: 0.197

Asia WGS AF: 0.231 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.4
DANN	Benign	0.40

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12485068; hg19: chr22-24234934;