chr11-15333700-T-C

Variant names:

• chr11-15333700-T-C
• rs11605083

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 0.179 in 152,238 control chromosomes in the GnomAD database, including 2,745 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 0.18 (2745 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.222 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: 0.180 AC: 27326 AN: 152120 Hom.: 2744 Cov.: 33

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.179 AC: 27326 AN: 152238 Hom.: 2745 Cov.: 33 AF XY: 0.178 AC XY: 13268 AN XY: 74436

African (AFR) AF: 0.101 AC: 4212 AN: 41560

American (AMR) AF: 0.164 AC: 2501 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 734 AN: 3472

East Asian (EAS) AF: 0.211 AC: 1089 AN: 5160

South Asian (SAS) AF: 0.225 AC: 1085 AN: 4822

European-Finnish (FIN) AF: 0.171 AC: 1816 AN: 10614

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

European-Non Finnish (NFE) AF: 0.225 AC: 15321 AN: 68006

Other (OTH) AF: 0.198 AC: 419 AN: 2112

Alfa AF: 0.210 Hom.: 10526

Bravo AF: 0.176

Asia WGS AF: 0.172 AC: 597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	3.1
DANN	Benign	0.25
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs11605083; hg19: chr11-15355246;