rs1250233

Variant names:

• chr2-215442380-G-A
• rs1250233

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.285 AC: 11811 AN: 41488

American (AMR) AF: 0.426 AC: 6519 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1202 AN: 3470

East Asian (EAS) AF: 0.918 AC: 4759 AN: 5182

South Asian (SAS) AF: 0.238 AC: 1145 AN: 4818

European-Finnish (FIN) AF: 0.283 AC: 2993 AN: 10590

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15435 AN: 67996

Other (OTH) AF: 0.322 AC: 680 AN: 2114

Alfa AF: 0.263 Hom.: 24106

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
PhyloP100		-0.037

Splicing

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

Other links and lift over

dbSNP: rs1250233; hg19: chr2-216307103;