11-92988621-A-C

Position:

• chr11-92988621-A-C

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 0.557 in 151,918 control chromosomes in the GnomAD database, including 23,939 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 0.56 (23939 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 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: 0.557 AC: 84560 AN: 151800 Hom.: 23907 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.557 AC: 84655 AN: 151918 Hom.: 23939 Cov.: 32 AF XY: 0.565 AC XY: 41987 AN XY: 74264

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.657

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.688

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.541

Alfa AF: 0.421 Hom.: 1182

Bravo AF: 0.565

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.9
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4406791; hg19: chr11-92721787;