11-92219378-A-G

Position:

• chr11-92219378-A-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 0.787 in 152,172 control chromosomes in the GnomAD database, including 47,332 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 (47332 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.826 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: 119721 AN: 152054 Hom.: 47284 Cov.: 33

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: 0.837

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.844

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.787 AC: 119827 AN: 152172 Hom.: 47332 Cov.: 33 AF XY: 0.784 AC XY: 58340 AN XY: 74368

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.838

Gnomad4 ASJ AF: 0.802

Gnomad4 EAS AF: 0.617

Gnomad4 SAS AF: 0.838

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.781

Gnomad4 OTH AF: 0.789

Alfa AF: 0.779 Hom.: 10231

Bravo AF: 0.795

Asia WGS AF: 0.742 AC: 2581 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501784; hg19: chr11-91952544;