rs9552733

chr13-22838784-G-Achr13-22838784-G-Cchr13-22838784-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 0.375 in 151,968 control chromosomes in the GnomAD database, including 11,426 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 0.38 (11426 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.244

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.499 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: 0.375 AC: 56988 AN: 151850 Hom.: 11427 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.375 AC: 57012 AN: 151968 Hom.: 11426 Cov.: 32 AF XY: 0.377 AC XY: 27965 AN XY: 74262

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.516

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.443

Gnomad4 OTH AF: 0.382

Alfa AF: 0.391 Hom.: 8091

Bravo AF: 0.355

Asia WGS AF: 0.389 AC: 1355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.6
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9552733; hg19: chr13-23412923; COSMIC: COSV69964152;