rs2133890

Positions:

• chr3-193820088-A-G

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 0.0124 in 152,330 control chromosomes in the GnomAD database, including 14 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 0.012 (14 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0124 (1896/152330) while in subpopulation SAS AF= 0.0207 (100/4830). AF 95% confidence interval is 0.0182. There are 14 homozygotes in gnomad4. There are 893 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 14 gene

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: 0.0125 AC: 1898 AN: 152212 Hom.: 14 Cov.: 33

Gnomad AFR AF: 0.00311

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0102

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0207

Gnomad FIN AF: 0.0107

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0191

Gnomad OTH AF: 0.0124

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

GnomAD4 genome AF: 0.0124 AC: 1896 AN: 152330 Hom.: 14 Cov.: 33 AF XY: 0.0120 AC XY: 893 AN XY: 74492

Gnomad4 AFR AF: 0.00308

Gnomad4 AMR AF: 0.0103

Gnomad4 ASJ AF: 0.0179

Gnomad4 EAS AF: 0.000770

Gnomad4 SAS AF: 0.0207

Gnomad4 FIN AF: 0.0107

Gnomad4 NFE AF: 0.0191

Gnomad4 OTH AF: 0.0118

Alfa AF: 0.0168 Hom.: 6

Bravo AF: 0.0117

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.9
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2133890; hg19: chr3-193537877;