13-52208449-A-G

Position:

• chr13-52208449-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.941 in 152,126 control chromosomes in the GnomAD database, including 67,448 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 0.94 (67448 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.941 AC: 143106 AN: 152008 Hom.: 67397 Cov.: 29

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.947

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.940

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

GnomAD4 genome AF: 0.941 AC: 143216 AN: 152126 Hom.: 67448 Cov.: 29 AF XY: 0.943 AC XY: 70144 AN XY: 74364

Gnomad4 AFR AF: 0.960

Gnomad4 AMR AF: 0.961

Gnomad4 ASJ AF: 0.909

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.947

Gnomad4 FIN AF: 0.938

Gnomad4 NFE AF: 0.923

Gnomad4 OTH AF: 0.939

Alfa AF: 0.926 Hom.: 29426

Bravo AF: 0.945

Asia WGS AF: 0.954 AC: 3316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2094354; hg19: chr13-52782584;