12-22034857-A-G

Variant names:

• chr12-22034857-A-G
• rs11046263

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 0.218 in 152,168 control chromosomes in the GnomAD database, including 4,926 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 0.22 (4926 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.349
• 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 (EAS) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.218 AC: 33123 AN: 152050 Hom.: 4930 Cov.: 32

Gnomad AFR AF: 0.0566

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.218 AC: 33117 AN: 152168 Hom.: 4926 Cov.: 32 AF XY: 0.231 AC XY: 17217 AN XY: 74384

African (AFR) AF: 0.0565 AC: 2347 AN: 41560

American (AMR) AF: 0.258 AC: 3937 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 555 AN: 3470

East Asian (EAS) AF: 0.564 AC: 2906 AN: 5152

South Asian (SAS) AF: 0.350 AC: 1688 AN: 4822

European-Finnish (FIN) AF: 0.444 AC: 4698 AN: 10576

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16366 AN: 67990

Other (OTH) AF: 0.200 AC: 424 AN: 2116

Alfa AF: 0.220 Hom.: 1582

Bravo AF: 0.194

Asia WGS AF: 0.439 AC: 1526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.5
DANN	Benign	0.71
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs11046263; hg19: chr12-22187791;