11-15105602-G-C

Variant names:

• chr11-15105602-G-C
• rs11023434

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 0.199 in 152,208 control chromosomes in the GnomAD database, including 3,652 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 0.20 (3652 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.300
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30295 AN: 152090 Hom.: 3646 Cov.: 33

Gnomad AFR AF: 0.0919

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.199 AC: 30314 AN: 152208 Hom.: 3652 Cov.: 33 AF XY: 0.200 AC XY: 14909 AN XY: 74432

African (AFR) AF: 0.0916 AC: 3804 AN: 41538

American (AMR) AF: 0.352 AC: 5373 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 571 AN: 3470

East Asian (EAS) AF: 0.200 AC: 1034 AN: 5176

South Asian (SAS) AF: 0.270 AC: 1305 AN: 4828

European-Finnish (FIN) AF: 0.128 AC: 1357 AN: 10600

Middle Eastern (MID) AF: 0.202 AC: 59 AN: 292

European-Non Finnish (NFE) AF: 0.238 AC: 16162 AN: 68002

Other (OTH) AF: 0.205 AC: 433 AN: 2108

Alfa AF: 0.0691 Hom.: 87

Bravo AF: 0.210

Asia WGS AF: 0.217 AC: 756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	4.3
DANN	Benign	0.68
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs11023434; hg19: chr11-15127148;