rs9552680

chr13-22661146-C-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 0.326 in 151,916 control chromosomes in the GnomAD database, including 8,170 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 0.33 (8170 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.365 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: 0.326 AC: 49507 AN: 151798 Hom.: 8165 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.326 AC: 49531 AN: 151916 Hom.: 8170 Cov.: 32 AF XY: 0.330 AC XY: 24491 AN XY: 74224

Gnomad4 AFR AF: 0.341

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.329

Alfa AF: 0.311 Hom.: 1225

Bravo AF: 0.310

Asia WGS AF: 0.358 AC: 1248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.84
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9552680; hg19: chr13-23235285;