rs726039

chr13-104497103-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;