11-117878129-C-G

Variant names:

• chr11-117878129-C-G
• rs11605223

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 0.343 in 152,154 control chromosomes in the GnomAD database, including 10,995 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 0.34 (10995 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.469 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: 0.344 AC: 52240 AN: 152036 Hom.: 10994 Cov.: 33

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.343 AC: 52245 AN: 152154 Hom.: 10995 Cov.: 33 AF XY: 0.344 AC XY: 25572 AN XY: 74372

African (AFR) AF: 0.117 AC: 4865 AN: 41558

American (AMR) AF: 0.371 AC: 5680 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1092 AN: 3472

East Asian (EAS) AF: 0.122 AC: 634 AN: 5182

South Asian (SAS) AF: 0.259 AC: 1249 AN: 4830

European-Finnish (FIN) AF: 0.511 AC: 5386 AN: 10544

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32158 AN: 67958

Other (OTH) AF: 0.366 AC: 773 AN: 2110

Alfa AF: 0.399 Hom.: 1669

Bravo AF: 0.327

Asia WGS AF: 0.158 AC: 551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.1
DANN	Benign	0.73
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs11605223; hg19: chr11-117748844;