rs12288023

Variant names:

• chr11-67653870-T-C
• rs12288023

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 0.083 in 151,518 control chromosomes in the GnomAD database, including 553 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 0.083 (553 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.436
• Publications: 12 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 (EAS) allele frequency at 95% confidence interval = 0.115 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: 0.0831 AC: 12578 AN: 151402 Hom.: 555 Cov.: 31

Gnomad AFR AF: 0.0934

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.0774

Gnomad ASJ AF: 0.0456

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.0396

Gnomad FIN AF: 0.0559

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0842

Gnomad OTH AF: 0.0890

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

GnomAD4 genome AF: 0.0830 AC: 12580 AN: 151518 Hom.: 553 Cov.: 31 AF XY: 0.0826 AC XY: 6115 AN XY: 73988

African (AFR) AF: 0.0933 AC: 3849 AN: 41274

American (AMR) AF: 0.0773 AC: 1173 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.0456 AC: 158 AN: 3466

East Asian (EAS) AF: 0.123 AC: 635 AN: 5144

South Asian (SAS) AF: 0.0395 AC: 189 AN: 4790

European-Finnish (FIN) AF: 0.0559 AC: 585 AN: 10460

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0842 AC: 5718 AN: 67906

Other (OTH) AF: 0.0881 AC: 185 AN: 2100

Alfa AF: 0.0841 Hom.: 816

Bravo AF: 0.0849

Asia WGS AF: 0.0910 AC: 319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.7
DANN	Benign	0.47
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs12288023; hg19: chr11-67421341;