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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.751

Gnomad4 FIN AF: 0.697

Gnomad4 NFE AF: 0.728

Gnomad4 OTH AF: 0.707

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1833219; hg19: chr2-67297409;