11-106414942-C-T

Variant names:

• chr11-106414942-C-T
• rs17552029

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 0.0489 in 152,032 control chromosomes in the GnomAD database, including 232 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 0.049 (232 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.824
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0918 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0490 AC: 7443 AN: 151914 Hom.: 231 Cov.: 32

Gnomad AFR AF: 0.0493

Gnomad AMI AF: 0.0473

Gnomad AMR AF: 0.0433

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.0171

Gnomad SAS AF: 0.0993

Gnomad FIN AF: 0.0106

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0545

Gnomad OTH AF: 0.0497

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

GnomAD4 genome AF: 0.0489 AC: 7438 AN: 152032 Hom.: 232 Cov.: 32 AF XY: 0.0471 AC XY: 3499 AN XY: 74320

African (AFR) AF: 0.0493 AC: 2043 AN: 41452

American (AMR) AF: 0.0432 AC: 660 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0493 AC: 171 AN: 3470

East Asian (EAS) AF: 0.0172 AC: 89 AN: 5178

South Asian (SAS) AF: 0.0992 AC: 478 AN: 4820

European-Finnish (FIN) AF: 0.0106 AC: 112 AN: 10540

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0545 AC: 3705 AN: 67988

Other (OTH) AF: 0.0482 AC: 102 AN: 2114

Alfa AF: 0.0540 Hom.: 758

Bravo AF: 0.0502

Asia WGS AF: 0.0540 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.0
DANN	Benign	0.36
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs17552029; hg19: chr11-106285669;