rs11607526

Positions:

• chr11-59398929-G-A
• chr11-59398929-G-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 0.185 in 151,672 control chromosomes in the GnomAD database, including 3,230 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 0.19 (3230 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.455

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.263 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: 0.186 AC: 28119 AN: 151554 Hom.: 3233 Cov.: 31

Gnomad AFR AF: 0.0626

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.185 AC: 28120 AN: 151672 Hom.: 3230 Cov.: 31 AF XY: 0.182 AC XY: 13461 AN XY: 74088

Gnomad4 AFR AF: 0.0626

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.193

Alfa AF: 0.230 Hom.: 4159

Bravo AF: 0.172

Asia WGS AF: 0.152 AC: 526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.73
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11607526; hg19: chr11-59166402;