11-117946561-A-G

Variant names:

• chr11-117946561-A-G
• rs2515795

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.771 AC: 31949 AN: 41430

American (AMR) AF: 0.560 AC: 8546 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2039 AN: 3470

East Asian (EAS) AF: 0.307 AC: 1589 AN: 5172

South Asian (SAS) AF: 0.554 AC: 2666 AN: 4808

European-Finnish (FIN) AF: 0.633 AC: 6689 AN: 10564

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.576 AC: 39123 AN: 67946

Other (OTH) AF: 0.595 AC: 1256 AN: 2112

Alfa AF: 0.586 Hom.: 75830

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
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs2515795; hg19: chr11-117817276;