11-106286677-G-T

Variant names:

• chr11-106286677-G-T
• rs488212

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 0.153 in 152,064 control chromosomes in the GnomAD database, including 1,990 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 0.15 (1990 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 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: 0.153 AC: 23293 AN: 151946 Hom.: 1986 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.0709

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.153 AC: 23318 AN: 152064 Hom.: 1990 Cov.: 32 AF XY: 0.152 AC XY: 11286 AN XY: 74328

African (AFR) AF: 0.200 AC: 8287 AN: 41454

American (AMR) AF: 0.165 AC: 2523 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 710 AN: 3468

East Asian (EAS) AF: 0.324 AC: 1669 AN: 5152

South Asian (SAS) AF: 0.160 AC: 769 AN: 4820

European-Finnish (FIN) AF: 0.0709 AC: 751 AN: 10588

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8007 AN: 67988

Other (OTH) AF: 0.179 AC: 379 AN: 2116

Alfa AF: 0.135 Hom.: 5768

Bravo AF: 0.164

Asia WGS AF: 0.249 AC: 868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.40
DANN	Benign	0.43
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs488212; hg19: chr11-106157404;