chr11-116529665-A-G

Position:

• chr11-116529665-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 0.193 in 152,110 control chromosomes in the GnomAD database, including 2,974 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 0.19 (2974 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29378 AN: 151992 Hom.: 2973 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.0331

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.193 AC: 29380 AN: 152110 Hom.: 2974 Cov.: 32 AF XY: 0.192 AC XY: 14268 AN XY: 74384

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.0330

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.225

Alfa AF: 0.217 Hom.: 5029

Bravo AF: 0.192

Asia WGS AF: 0.113 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.51
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7941534; hg19: chr11-116400382;