rs133552

chr22-48239633-G-Cchr22-48239633-G-T

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 0.00767 in 152,268 control chromosomes in the GnomAD database, including 12 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 0.0077 (12 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00767 (1168/152268) while in subpopulation SAS AF= 0.0284 (137/4818). AF 95% confidence interval is 0.0246. There are 12 homozygotes in gnomad4. There are 601 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 12 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: 0.00767 AC: 1167 AN: 152150 Hom.: 12 Cov.: 33

Gnomad AFR AF: 0.00159

Gnomad AMI AF: 0.0308

Gnomad AMR AF: 0.00812

Gnomad ASJ AF: 0.0193

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0282

Gnomad FIN AF: 0.00311

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0101

Gnomad OTH AF: 0.00911

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

GnomAD4 genome AF: 0.00767 AC: 1168 AN: 152268 Hom.: 12 Cov.: 33 AF XY: 0.00807 AC XY: 601 AN XY: 74440

Gnomad4 AFR AF: 0.00159

Gnomad4 AMR AF: 0.00811

Gnomad4 ASJ AF: 0.0193

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0284

Gnomad4 FIN AF: 0.00311

Gnomad4 NFE AF: 0.0101

Gnomad4 OTH AF: 0.00901

Alfa AF: 0.00306 Hom.: 0

Bravo AF: 0.00737

Asia WGS AF: 0.00808 AC: 28 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.3
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs133552; hg19: chr22-48635445;