chr11-93076039-G-T

Position:

• chr11-93076039-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 0.424 in 150,788 control chromosomes in the GnomAD database, including 14,417 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 0.42 (14417 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.558 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: 0.424 AC: 63849 AN: 150662 Hom.: 14412 Cov.: 33

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.800

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.575

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.424 AC: 63879 AN: 150788 Hom.: 14417 Cov.: 33 AF XY: 0.430 AC XY: 31699 AN XY: 73700

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.575

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.424

Alfa AF: 0.425 Hom.: 6933

Bravo AF: 0.413

Asia WGS AF: 0.490 AC: 1706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.4
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1876602; hg19: chr11-92809205;