11-34583888-T-G

Position:

• chr11-34583888-T-G

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 0.713 in 152,154 control chromosomes in the GnomAD database, including 39,527 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 0.71 (39527 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.796 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: 0.713 AC: 108456 AN: 152036 Hom.: 39507 Cov.: 33

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.782

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.713 AC: 108526 AN: 152154 Hom.: 39527 Cov.: 33 AF XY: 0.711 AC XY: 52859 AN XY: 74382

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.737

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.782

Gnomad4 NFE AF: 0.802

Gnomad4 OTH AF: 0.727

Alfa AF: 0.776 Hom.: 90419

Bravo AF: 0.698

Asia WGS AF: 0.601 AC: 2091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.0
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5028798; hg19: chr11-34605435;