rs13253111

Variant names:

• chr8-28204457-A-G
• rs13253111

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 0.366 in 152,134 control chromosomes in the GnomAD database, including 11,266 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 0.37 (11266 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358

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 = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55681 AN: 152016 Hom.: 11264 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.366 AC: 55709 AN: 152134 Hom.: 11266 Cov.: 32 AF XY: 0.366 AC XY: 27183 AN XY: 74366

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.394

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.401

Alfa AF: 0.421 Hom.: 6938

Bravo AF: 0.365

Asia WGS AF: 0.472 AC: 1640 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	1.1
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13253111; hg19: chr8-28061974;