rs1275051

Positions:

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

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 0.659 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.802

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.676

Alfa AF: 0.630 Hom.: 9082

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1275051; hg19: chr11-123547170;