rs1833219

Variant names:

• chr2-67070277-A-C
• rs1833219

Your query was ambiguous. Multiple possible variants found:

• chr2-67070277-A-C
• chr2-67070277-A-G
• chr2-67070277-A-T

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 0.709 in 152,012 control chromosomes in the GnomAD database, including 38,427 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 0.71 (38427 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.807 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: 0.709 AC: 107760 AN: 151894 Hom.: 38414 Cov.: 33

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.709 AC: 107823 AN: 152012 Hom.: 38427 Cov.: 33 AF XY: 0.709 AC XY: 52666 AN XY: 74270

African (AFR) AF: 0.664 AC: 27554 AN: 41492

American (AMR) AF: 0.699 AC: 10671 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2485 AN: 3468

East Asian (EAS) AF: 0.827 AC: 4245 AN: 5130

South Asian (SAS) AF: 0.751 AC: 3618 AN: 4820

European-Finnish (FIN) AF: 0.697 AC: 7378 AN: 10592

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.728 AC: 49430 AN: 67938

Other (OTH) AF: 0.707 AC: 1492 AN: 2110

Alfa AF: 0.631 Hom.: 1831

Bravo AF: 0.707

Asia WGS AF: 0.762 AC: 2652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.82
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs1833219; hg19: chr2-67297409;