rs13288553

Positions:

• chr9-84126546-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 0.109 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;