11-117946561-A-G

Position:

• chr11-117946561-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 0.621 in 151,978 control chromosomes in the GnomAD database, including 30,172 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 0.62 (30172 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.455

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 (AFR) allele frequency at 95% confidence interval = 0.764 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: 0.621 AC: 94324 AN: 151860 Hom.: 30122 Cov.: 31

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.576

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.621 AC: 94451 AN: 151978 Hom.: 30172 Cov.: 31 AF XY: 0.617 AC XY: 45865 AN XY: 74288

Gnomad4 AFR AF: 0.771

Gnomad4 AMR AF: 0.560

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.576

Gnomad4 OTH AF: 0.595

Alfa AF: 0.573 Hom.: 23033

Bravo AF: 0.620

Asia WGS AF: 0.483 AC: 1684 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	6.1
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2515795; hg19: chr11-117817276;