11-59398929-G-A

Variant names:

• chr11-59398929-G-A
• rs11607526

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 0.185 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.0626 AC: 2595 AN: 41456

American (AMR) AF: 0.138 AC: 2092 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 813 AN: 3464

East Asian (EAS) AF: 0.120 AC: 614 AN: 5126

South Asian (SAS) AF: 0.164 AC: 789 AN: 4812

European-Finnish (FIN) AF: 0.249 AC: 2627 AN: 10552

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.266 AC: 18048 AN: 67762

Other (OTH) AF: 0.193 AC: 407 AN: 2106

Alfa AF: 0.222 Hom.: 5208

Bravo AF: 0.172

Asia WGS AF: 0.152 AC: 526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.73
DANN	Benign	0.76
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs11607526; hg19: chr11-59166402;