rs726039

Variant names:

• chr13-104497103-G-A
• rs726039

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 0.083 in 151,964 control chromosomes in the GnomAD database, including 679 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 0.083 (679 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340

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 = 0.151 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: 0.0830 AC: 12609 AN: 151846 Hom.: 680 Cov.: 33

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0675

Gnomad ASJ AF: 0.0968

Gnomad EAS AF: 0.0838

Gnomad SAS AF: 0.0910

Gnomad FIN AF: 0.0129

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0529

Gnomad OTH AF: 0.0994

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

GnomAD4 genome AF: 0.0830 AC: 12610 AN: 151964 Hom.: 679 Cov.: 33 AF XY: 0.0808 AC XY: 5998 AN XY: 74270

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.0673

Gnomad4 ASJ AF: 0.0968

Gnomad4 EAS AF: 0.0841

Gnomad4 SAS AF: 0.0898

Gnomad4 FIN AF: 0.0129

Gnomad4 NFE AF: 0.0529

Gnomad4 OTH AF: 0.0984

Alfa AF: 0.0649 Hom.: 533

Bravo AF: 0.0901

Asia WGS AF: 0.0760 AC: 262 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs726039; hg19: chr13-105149453;