rs1275051

Variant names:

• chr11-123676462-G-A
• rs1275051

Your query was ambiguous. Multiple possible variants found:

• chr11-123676462-G-A
• chr11-123676462-G-C

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 0.659 in 152,050 control chromosomes in the GnomAD database, including 33,130 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 0.66 (33130 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.698
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.707 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: 0.659 AC: 100185 AN: 151932 Hom.: 33104 Cov.: 32

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.659 AC: 100256 AN: 152050 Hom.: 33130 Cov.: 32 AF XY: 0.663 AC XY: 49291 AN XY: 74294

African (AFR) AF: 0.670 AC: 27791 AN: 41460

American (AMR) AF: 0.718 AC: 10970 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2782 AN: 3470

East Asian (EAS) AF: 0.676 AC: 3495 AN: 5172

South Asian (SAS) AF: 0.701 AC: 3370 AN: 4808

European-Finnish (FIN) AF: 0.636 AC: 6719 AN: 10560

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42777 AN: 67974

Other (OTH) AF: 0.676 AC: 1430 AN: 2116

Alfa AF: 0.638 Hom.: 11840

Bravo AF: 0.669

Asia WGS AF: 0.655 AC: 2282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.62
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs1275051; hg19: chr11-123547170;