rs1559759

Variant names:

• chr11-35101504-C-A
• rs1559759

Your query was ambiguous. Multiple possible variants found:

• chr11-35101504-C-A
• chr11-35101504-C-G
• chr11-35101504-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 0.149 in 152,164 control chromosomes in the GnomAD database, including 1,896 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 0.15 (1896 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 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: 0.149 AC: 22632 AN: 152046 Hom.: 1900 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.149 AC: 22628 AN: 152164 Hom.: 1896 Cov.: 32 AF XY: 0.152 AC XY: 11314 AN XY: 74378

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.161

Alfa AF: 0.154 Hom.: 4089

Bravo AF: 0.143

Asia WGS AF: 0.270 AC: 937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	13
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1559759; hg19: chr11-35123051;