11-106286677-G-T

Variant names:

• chr11-106286677-G-T
• rs488212

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.153 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

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.0709

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.179

Alfa AF: 0.135 Hom.: 2446

Bravo AF: 0.164

Asia WGS AF: 0.249 AC: 868 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs488212; hg19: chr11-106157404;