11-58806534-A-G

Variant names:

• chr11-58806534-A-G
• rs10501373

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 0.0337 in 151,974 control chromosomes in the GnomAD database, including 189 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 0.034 (189 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.893

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 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: 0.0336 AC: 5104 AN: 151856 Hom.: 187 Cov.: 32

Gnomad AFR AF: 0.0267

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0442

Gnomad ASJ AF: 0.0251

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0242

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0195

Gnomad OTH AF: 0.0331

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

GnomAD4 genome AF: 0.0337 AC: 5115 AN: 151974 Hom.: 189 Cov.: 32 AF XY: 0.0366 AC XY: 2720 AN XY: 74276

Gnomad4 AFR AF: 0.0267

Gnomad4 AMR AF: 0.0446

Gnomad4 ASJ AF: 0.0251

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.0242

Gnomad4 NFE AF: 0.0195

Gnomad4 OTH AF: 0.0327

Alfa AF: 0.00940 Hom.: 1

Bravo AF: 0.0360

Asia WGS AF: 0.130 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.3
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501373; hg19: chr11-58574007;