rs11686135

Variant names:

• chr2-4271386-T-C
• rs11686135

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 0.113 in 152,000 control chromosomes in the GnomAD database, including 1,039 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 0.11 (1039 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.742
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.138 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: 0.114 AC: 17249 AN: 151882 Hom.: 1038 Cov.: 31

Gnomad AFR AF: 0.0937

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0801

Gnomad FIN AF: 0.0819

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.113 AC: 17251 AN: 152000 Hom.: 1039 Cov.: 31 AF XY: 0.110 AC XY: 8196 AN XY: 74322

African (AFR) AF: 0.0937 AC: 3883 AN: 41454

American (AMR) AF: 0.106 AC: 1618 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 550 AN: 3468

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5178

South Asian (SAS) AF: 0.0797 AC: 385 AN: 4828

European-Finnish (FIN) AF: 0.0819 AC: 863 AN: 10532

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9547 AN: 67956

Other (OTH) AF: 0.102 AC: 216 AN: 2112

Alfa AF: 0.130 Hom.: 1808

Bravo AF: 0.112

Asia WGS AF: 0.0390 AC: 135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	11
DANN	Benign	0.89
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs11686135; hg19: chr2-4318976;