chr13-25137199-G-A

Variant names:

• chr13-25137199-G-A
• rs9511655

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 0.0898 in 152,218 control chromosomes in the GnomAD database, including 1,046 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 0.090 (1046 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.840
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 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: 0.0899 AC: 13670 AN: 152100 Hom.: 1047 Cov.: 33

Gnomad AFR AF: 0.0278

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0858

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0898 AC: 13668 AN: 152218 Hom.: 1046 Cov.: 33 AF XY: 0.0936 AC XY: 6969 AN XY: 74418

African (AFR) AF: 0.0277 AC: 1150 AN: 41544

American (AMR) AF: 0.179 AC: 2743 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0620 AC: 215 AN: 3470

East Asian (EAS) AF: 0.345 AC: 1783 AN: 5170

South Asian (SAS) AF: 0.119 AC: 574 AN: 4814

European-Finnish (FIN) AF: 0.102 AC: 1082 AN: 10594

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0858 AC: 5838 AN: 68016

Other (OTH) AF: 0.107 AC: 226 AN: 2110

Alfa AF: 0.0965 Hom.: 1073

Bravo AF: 0.0985

Asia WGS AF: 0.209 AC: 727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.1
DANN	Benign	0.61
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs9511655; hg19: chr13-25711337;