chr11-92218988-G-A

Position:

• chr11-92218988-G-A

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 0.787 in 152,100 control chromosomes in the GnomAD database, including 47,291 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 0.79 (47291 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.825 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: 0.787 AC: 119660 AN: 151982 Hom.: 47247 Cov.: 32

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.787 AC: 119762 AN: 152100 Hom.: 47291 Cov.: 32 AF XY: 0.785 AC XY: 58335 AN XY: 74358

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.837

Gnomad4 ASJ AF: 0.802

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.839

Gnomad4 FIN AF: 0.707

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.788

Alfa AF: 0.773 Hom.: 35094

Bravo AF: 0.795

Asia WGS AF: 0.741 AC: 2575 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	12
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1350445; hg19: chr11-91952154;