rs11265263

Variant names:

• chr1-159740727-C-A
• rs11265263

Your query was ambiguous. Multiple possible variants found:

• chr1-159740727-C-A
• chr1-159740727-C-T

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 0.0642 in 152,154 control chromosomes in the GnomAD database, including 426 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 0.064 (426 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.728
• Publications: 19 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 (EAS) allele frequency at 95% confidence interval = 0.183 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: 0.0642 AC: 9767 AN: 152036 Hom.: 425 Cov.: 31

Gnomad AFR AF: 0.0258

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0643

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.0906

Gnomad FIN AF: 0.0764

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0710

Gnomad OTH AF: 0.0771

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

GnomAD4 genome AF: 0.0642 AC: 9768 AN: 152154 Hom.: 426 Cov.: 31 AF XY: 0.0648 AC XY: 4821 AN XY: 74382

African (AFR) AF: 0.0258 AC: 1073 AN: 41534

American (AMR) AF: 0.0643 AC: 982 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 407 AN: 3472

East Asian (EAS) AF: 0.193 AC: 997 AN: 5172

South Asian (SAS) AF: 0.0913 AC: 440 AN: 4818

European-Finnish (FIN) AF: 0.0764 AC: 808 AN: 10578

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0710 AC: 4828 AN: 67992

Other (OTH) AF: 0.0773 AC: 163 AN: 2110

Alfa AF: 0.0709 Hom.: 1237

Bravo AF: 0.0620

Asia WGS AF: 0.158 AC: 550 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.4
DANN	Benign	0.66
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs11265263; hg19: chr1-159710517;