rs9511655

chr13-25137199-G-Achr13-25137199-G-T

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 0.0898 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0277

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.0620

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.0858

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0972 Hom.: 820

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9511655; hg19: chr13-25711337;