chr13-104497103-G-A

Variant names:

• chr13-104497103-G-A
• rs726039

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.154 AC: 6385 AN: 41456

American (AMR) AF: 0.0673 AC: 1027 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0968 AC: 336 AN: 3470

East Asian (EAS) AF: 0.0841 AC: 435 AN: 5170

South Asian (SAS) AF: 0.0898 AC: 433 AN: 4820

European-Finnish (FIN) AF: 0.0129 AC: 136 AN: 10568

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0529 AC: 3594 AN: 67904

Other (OTH) AF: 0.0984 AC: 208 AN: 2114

Alfa AF: 0.0655 Hom.: 1235

Bravo AF: 0.0901

Asia WGS AF: 0.0760 AC: 262 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.59
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs726039; hg19: chr13-105149453;