chr11-117878400-G-C

Variant names:

• chr11-117878400-G-C
• rs3809043

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 0.0472 in 152,226 control chromosomes in the GnomAD database, including 193 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 0.047 (193 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.550
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0472 AC: 7183 AN: 152108 Hom.: 193 Cov.: 33

Gnomad AFR AF: 0.0601

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0384

Gnomad ASJ AF: 0.0556

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.0728

Gnomad FIN AF: 0.00896

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0387

Gnomad OTH AF: 0.0602

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

GnomAD4 genome AF: 0.0472 AC: 7179 AN: 152226 Hom.: 193 Cov.: 33 AF XY: 0.0465 AC XY: 3462 AN XY: 74420

African (AFR) AF: 0.0599 AC: 2489 AN: 41522

American (AMR) AF: 0.0383 AC: 586 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0556 AC: 193 AN: 3470

East Asian (EAS) AF: 0.114 AC: 588 AN: 5166

South Asian (SAS) AF: 0.0726 AC: 350 AN: 4820

European-Finnish (FIN) AF: 0.00896 AC: 95 AN: 10606

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0387 AC: 2629 AN: 68020

Other (OTH) AF: 0.0600 AC: 127 AN: 2116

Alfa AF: 0.0407 Hom.: 16

Bravo AF: 0.0511

Asia WGS AF: 0.0740 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.65
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs3809043; hg19: chr11-117749115;