rs12422135

Variant names:

• chr11-69563968-A-G
• rs12422135

Your query was ambiguous. Multiple possible variants found:

• chr11-69563968-A-G
• chr11-69563968-A-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 0.432 in 152,164 control chromosomes in the GnomAD database, including 17,226 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 0.43 (17226 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.163
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65713 AN: 152046 Hom.: 17224 Cov.: 33

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.432 AC: 65717 AN: 152164 Hom.: 17226 Cov.: 33 AF XY: 0.431 AC XY: 32074 AN XY: 74388

African (AFR) AF: 0.150 AC: 6246 AN: 41530

American (AMR) AF: 0.385 AC: 5884 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1732 AN: 3472

East Asian (EAS) AF: 0.234 AC: 1210 AN: 5178

South Asian (SAS) AF: 0.489 AC: 2357 AN: 4822

European-Finnish (FIN) AF: 0.643 AC: 6795 AN: 10564

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39811 AN: 67984

Other (OTH) AF: 0.436 AC: 922 AN: 2114

Alfa AF: 0.524 Hom.: 35478

Bravo AF: 0.399

Asia WGS AF: 0.359 AC: 1250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.48
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs12422135; hg19: chr11-69378736;