rs13255059

chr8-127518371-A-Gchr8-127518371-A-T

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 0.909 in 152,174 control chromosomes in the GnomAD database, including 62,940 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 0.91 (62940 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.932 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: 0.909 AC: 138188 AN: 152056 Hom.: 62892 Cov.: 33

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.929

Gnomad ASJ AF: 0.938

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.868

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.920

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

GnomAD4 genome AF: 0.909 AC: 138292 AN: 152174 Hom.: 62940 Cov.: 33 AF XY: 0.906 AC XY: 67388 AN XY: 74374

Gnomad4 AFR AF: 0.940

Gnomad4 AMR AF: 0.928

Gnomad4 ASJ AF: 0.938

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.868

Gnomad4 FIN AF: 0.838

Gnomad4 NFE AF: 0.901

Gnomad4 OTH AF: 0.915

Alfa AF: 0.904 Hom.: 21463

Bravo AF: 0.916

Asia WGS AF: 0.833 AC: 2901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.5
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13255059; hg19: chr8-128530616;