11-106236286-T-G

Variant names:

• chr11-106236286-T-G
• rs7116622

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 0.098 in 152,142 control chromosomes in the GnomAD database, including 798 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 0.098 (798 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.142 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: 0.0978 AC: 14870 AN: 152024 Hom.: 788 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0825

Gnomad ASJ AF: 0.0841

Gnomad EAS AF: 0.00925

Gnomad SAS AF: 0.0961

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0771

Gnomad OTH AF: 0.0961

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

GnomAD4 genome AF: 0.0980 AC: 14912 AN: 152142 Hom.: 798 Cov.: 32 AF XY: 0.100 AC XY: 7435 AN XY: 74372

African (AFR) AF: 0.145 AC: 6017 AN: 41492

American (AMR) AF: 0.0824 AC: 1258 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0841 AC: 292 AN: 3470

East Asian (EAS) AF: 0.00927 AC: 48 AN: 5176

South Asian (SAS) AF: 0.0966 AC: 466 AN: 4824

European-Finnish (FIN) AF: 0.122 AC: 1295 AN: 10578

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.0770 AC: 5239 AN: 68008

Other (OTH) AF: 0.0960 AC: 203 AN: 2114

Alfa AF: 0.0376 Hom.: 19

Bravo AF: 0.0965

Asia WGS AF: 0.0600 AC: 208 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.82
PhyloP100		-0.096

Splicing

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

Other links and lift over

dbSNP: rs7116622; hg19: chr11-106107013;