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. Variant got -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

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 (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

Gnomad4 AFR AF: 0.0258

Gnomad4 AMR AF: 0.0643

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.0913

Gnomad4 FIN AF: 0.0764

Gnomad4 NFE AF: 0.0710

Gnomad4 OTH AF: 0.0773

Alfa AF: 0.0730 Hom.: 848

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11265263; hg19: chr1-159710517;