rs2233375

Variant names:

• chr2-233031788-C-T
• rs2233375

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 0.154 in 152,174 control chromosomes in the GnomAD database, including 2,360 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 0.15 (2360 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23464 AN: 152056 Hom.: 2354 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.0881

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.0611

Gnomad EAS AF: 0.0104

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0879

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.154 AC: 23500 AN: 152174 Hom.: 2360 Cov.: 33 AF XY: 0.152 AC XY: 11282 AN XY: 74412

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.0611

Gnomad4 EAS AF: 0.0104

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.0879

Gnomad4 NFE AF: 0.103

Gnomad4 OTH AF: 0.127

Alfa AF: 0.111 Hom.: 1135

Bravo AF: 0.164

Asia WGS AF: 0.0740 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2233375; hg19: chr2-233896498;