rs9533338

chr13-42996751-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0289 in 152,292 control chromosomes in the GnomAD database, including 83 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 0.029 (83 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.931

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0289 (4397/152292) while in subpopulation NFE AF= 0.0415 (2825/68012). AF 95% confidence interval is 0.0403. There are 83 homozygotes in gnomad4. There are 2181 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 83 gene

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: 0.0289 AC: 4397 AN: 152174 Hom.: 83 Cov.: 33

Gnomad AFR AF: 0.00646

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0360

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.0425

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0415

Gnomad OTH AF: 0.0315

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

GnomAD4 genome AF: 0.0289 AC: 4397 AN: 152292 Hom.: 83 Cov.: 33 AF XY: 0.0293 AC XY: 2181 AN XY: 74464

Gnomad4 AFR AF: 0.00645

Gnomad4 AMR AF: 0.0360

Gnomad4 ASJ AF: 0.0245

Gnomad4 EAS AF: 0.00173

Gnomad4 SAS AF: 0.0265

Gnomad4 FIN AF: 0.0425

Gnomad4 NFE AF: 0.0415

Gnomad4 OTH AF: 0.0312

Alfa AF: 0.0301 Hom.: 7

Bravo AF: 0.0269

Asia WGS AF: 0.0120 AC: 43 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.14
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9533338; hg19: chr13-43570887;