11-116792959-G-A

Position:

• chr11-116792959-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 0.0906 in 152,210 control chromosomes in the GnomAD database, including 819 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 0.091 (819 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.132 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: 0.0907 AC: 13793 AN: 152092 Hom.: 820 Cov.: 32

Gnomad AFR AF: 0.0279

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.0806

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.0906 AC: 13792 AN: 152210 Hom.: 819 Cov.: 32 AF XY: 0.0882 AC XY: 6565 AN XY: 74404

Gnomad4 AFR AF: 0.0278

Gnomad4 AMR AF: 0.0804

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.0228

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.105

Alfa AF: 0.102 Hom.: 141

Bravo AF: 0.0852

Asia WGS AF: 0.0140 AC: 49 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	9.5
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1729411; hg19: chr11-116663675;