rs12275055

Positions:

• chr11-69213892-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 0.119 in 152,232 control chromosomes in the GnomAD database, including 1,298 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 (1298 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.272

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.69213892A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18106 AN: 152114 Hom.: 1299 Cov.: 32

Gnomad AFR AF: 0.0591

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.0150

Gnomad SAS AF: 0.0777

Gnomad FIN AF: 0.0836

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.119 AC: 18099 AN: 152232 Hom.: 1298 Cov.: 32 AF XY: 0.115 AC XY: 8577 AN XY: 74442

Gnomad4 AFR AF: 0.0589

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.0147

Gnomad4 SAS AF: 0.0782

Gnomad4 FIN AF: 0.0836

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.151

Alfa AF: 0.154 Hom.: 473

Bravo AF: 0.120

Asia WGS AF: 0.0560 AC: 194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12275055; hg19: chr11-68981359;