11-106652498-A-G

Variant names:

• chr11-106652498-A-G
• rs12364992

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 0.0834 in 152,252 control chromosomes in the GnomAD database, including 719 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 0.083 (719 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.429
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0834 AC: 12681 AN: 152134 Hom.: 715 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.0896

Gnomad SAS AF: 0.0306

Gnomad FIN AF: 0.0512

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0476

Gnomad OTH AF: 0.0847

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

GnomAD4 genome AF: 0.0834 AC: 12693 AN: 152252 Hom.: 719 Cov.: 32 AF XY: 0.0836 AC XY: 6226 AN XY: 74444

African (AFR) AF: 0.137 AC: 5695 AN: 41532

American (AMR) AF: 0.148 AC: 2257 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0386 AC: 134 AN: 3470

East Asian (EAS) AF: 0.0900 AC: 465 AN: 5164

South Asian (SAS) AF: 0.0306 AC: 148 AN: 4830

European-Finnish (FIN) AF: 0.0512 AC: 544 AN: 10616

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0475 AC: 3235 AN: 68042

Other (OTH) AF: 0.0876 AC: 185 AN: 2112

Alfa AF: 0.0620 Hom.: 1092

Bravo AF: 0.0939

Asia WGS AF: 0.0700 AC: 241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.36
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs12364992; hg19: chr11-106523224;