13-85315505-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 0.587 in 151,668 control chromosomes in the GnomAD database, including 27,644 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 0.59 (27644 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.95

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.813 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: 0.587 AC: 88971 AN: 151548 Hom.: 27621 Cov.: 30

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.587 AC: 89020 AN: 151668 Hom.: 27644 Cov.: 30 AF XY: 0.595 AC XY: 44113 AN XY: 74108

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.834

Gnomad4 SAS AF: 0.648

Gnomad4 FIN AF: 0.762

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.578

Alfa AF: 0.524 Hom.: 1720

Bravo AF: 0.576

Asia WGS AF: 0.728 AC: 2533 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.042
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1571830; hg19: chr13-85889640;