chr13-22848383-T-G

Variant names:

• chr13-22848383-T-G
• rs11616753

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 0.244 in 152,134 control chromosomes in the GnomAD database, including 4,813 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 0.24 (4813 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.292 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: 0.244 AC: 37107 AN: 152016 Hom.: 4814 Cov.: 33

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.0202

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.244 AC: 37124 AN: 152134 Hom.: 4813 Cov.: 33 AF XY: 0.237 AC XY: 17622 AN XY: 74394

African (AFR) AF: 0.296 AC: 12283 AN: 41468

American (AMR) AF: 0.191 AC: 2920 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 986 AN: 3472

East Asian (EAS) AF: 0.0200 AC: 104 AN: 5188

South Asian (SAS) AF: 0.112 AC: 541 AN: 4816

European-Finnish (FIN) AF: 0.177 AC: 1871 AN: 10590

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17484 AN: 67988

Other (OTH) AF: 0.272 AC: 576 AN: 2114

Alfa AF: 0.251 Hom.: 2824

Bravo AF: 0.248

Asia WGS AF: 0.0810 AC: 283 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	8.7
DANN	Benign	0.14
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs11616753; hg19: chr13-23422522;