11-35595578-A-T

Variant names:

• chr11-35595578-A-T
• rs599389

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 0.468 in 151,816 control chromosomes in the GnomAD database, including 16,696 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 0.47 (16696 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.547 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: 0.468 AC: 70925 AN: 151698 Hom.: 16674 Cov.: 31

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.468 AC: 70992 AN: 151816 Hom.: 16696 Cov.: 31 AF XY: 0.469 AC XY: 34784 AN XY: 74190

Gnomad4 AFR AF: 0.500

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.451

Gnomad4 OTH AF: 0.427

Alfa AF: 0.455 Hom.: 1912

Bravo AF: 0.467

Asia WGS AF: 0.457 AC: 1586 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.5
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: rs599389; hg19: chr11-35617126;