rs1250233

Positions:

• chr2-215442380-G-A
• chr2-215442380-G-C

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 0.295 in 152,150 control chromosomes in the GnomAD database, including 8,104 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 0.29 (8104 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370

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 = 0.897 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: 0.295 AC: 44806 AN: 152032 Hom.: 8105 Cov.: 33

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.295 AC: 44819 AN: 152150 Hom.: 8104 Cov.: 33 AF XY: 0.303 AC XY: 22520 AN XY: 74382

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.918

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.322

Alfa AF: 0.261 Hom.: 10357

Bravo AF: 0.313

Asia WGS AF: 0.529 AC: 1839 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	1.0
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1250233; hg19: chr2-216307103;