rs12275055

Variant names:

• chr11-69213892-A-G
• rs12275055

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.272

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;