rs13288553

Variant names:

• chr9-84126546-G-T
• rs13288553

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 0.109 in 152,164 control chromosomes in the GnomAD database, including 1,163 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 0.11 (1163 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.587

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.162 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: 0.109 AC: 16530 AN: 152046 Hom.: 1159 Cov.: 32

Gnomad AFR AF: 0.0275

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0978

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.0371

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.109 AC: 16542 AN: 152164 Hom.: 1163 Cov.: 32 AF XY: 0.108 AC XY: 8000 AN XY: 74404

Gnomad4 AFR AF: 0.0275

Gnomad4 AMR AF: 0.0975

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.0368

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.122

Alfa AF: 0.135 Hom.: 188

Bravo AF: 0.0983

Asia WGS AF: 0.111 AC: 384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.7
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13288553; hg19: chr9-86741461; COSMIC: COSV60369936;