13-20201858-G-C

Variant names:

• chr13-20201858-G-C
• rs9552104

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 0.124 in 152,136 control chromosomes in the GnomAD database, including 1,758 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 0.12 (1758 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.408 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: 0.124 AC: 18873 AN: 152018 Hom.: 1749 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.0734

Gnomad FIN AF: 0.0321

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0641

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.124 AC: 18924 AN: 152136 Hom.: 1758 Cov.: 32 AF XY: 0.128 AC XY: 9489 AN XY: 74382

African (AFR) AF: 0.187 AC: 7760 AN: 41452

American (AMR) AF: 0.211 AC: 3221 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0945 AC: 328 AN: 3472

East Asian (EAS) AF: 0.423 AC: 2184 AN: 5168

South Asian (SAS) AF: 0.0735 AC: 354 AN: 4816

European-Finnish (FIN) AF: 0.0321 AC: 340 AN: 10602

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0641 AC: 4359 AN: 68026

Other (OTH) AF: 0.125 AC: 265 AN: 2112

Alfa AF: 0.0960 Hom.: 127

Bravo AF: 0.144

Asia WGS AF: 0.214 AC: 742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	0.75
DANN	Benign	0.90
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs9552104; hg19: chr13-20775997;