13-108055894-G-T

Variant names:

• chr13-108055894-G-T
• rs4325412

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 0.191 in 151,990 control chromosomes in the GnomAD database, including 2,963 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 0.19 (2963 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.234 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: 0.191 AC: 28951 AN: 151872 Hom.: 2958 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.191 AC: 28982 AN: 151990 Hom.: 2963 Cov.: 32 AF XY: 0.186 AC XY: 13815 AN XY: 74282

African (AFR) AF: 0.238 AC: 9864 AN: 41454

American (AMR) AF: 0.119 AC: 1824 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 649 AN: 3466

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5170

South Asian (SAS) AF: 0.106 AC: 507 AN: 4794

European-Finnish (FIN) AF: 0.173 AC: 1832 AN: 10570

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13810 AN: 67954

Other (OTH) AF: 0.156 AC: 330 AN: 2110

Alfa AF: 0.188 Hom.: 4956

Bravo AF: 0.188

Asia WGS AF: 0.0670 AC: 233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.26
DANN	Benign	0.52
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4325412; hg19: chr13-108708242;