chr11-116182567-G-A

Position:

• chr11-116182567-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 0.103 in 152,114 control chromosomes in the GnomAD database, including 985 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 0.10 (985 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.927

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.276 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: 0.103 AC: 15638 AN: 151996 Hom.: 983 Cov.: 32

Gnomad AFR AF: 0.0510

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.0993

Gnomad FIN AF: 0.0919

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.103 AC: 15648 AN: 152114 Hom.: 985 Cov.: 32 AF XY: 0.104 AC XY: 7705 AN XY: 74354

Gnomad4 AFR AF: 0.0511

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.0996

Gnomad4 FIN AF: 0.0919

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.122

Alfa AF: 0.0935 Hom.: 426

Bravo AF: 0.108

Asia WGS AF: 0.182 AC: 634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.5
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2251835; hg19: chr11-116053284;