rs2399153

Variant names:

• chr22-17012403-A-G
• rs2399153
• ENST00000605217.1:n.-1A>G

Your query was ambiguous. Multiple possible variants found:

• chr22-17012403-A-G
• chr22-17012403-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000605217.1(ENSG00000270226):​n.-1A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.879 in 153,664 control chromosomes in the GnomAD database, including 59,617 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 0.88 (59084 hom., cov: 31)
  • Exomes 𝑓: 0.83 (533 hom.)
• Consequence: ENSG00000270226 ENST00000605217.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875

Genes affected

ENSG00000270226 (HGNC:56970):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.961 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
ENSG00000270226	ENST00000605217.1	n.-1A>G		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.879 AC: 133659 AN: 152032 Hom.: 59030 Cov.: 31

Gnomad AFR AF: 0.969

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.903

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.872

GnomAD4 exome AF: 0.830 AC: 1256 AN: 1514 Hom.: 533 Cov.: 0 AF XY: 0.840 AC XY: 746 AN XY: 888

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 1.00

Gnomad4 ASJ exome AF: 0.900

Gnomad4 EAS exome AF: 0.750

Gnomad4 SAS exome AF: 0.799

Gnomad4 FIN exome AF: 0.869

Gnomad4 NFE exome AF: 0.867

Gnomad4 OTH exome AF: 0.766

GnomAD4 genome AF: 0.879 AC: 133776 AN: 152150 Hom.: 59084 Cov.: 31 AF XY: 0.883 AC XY: 65631 AN XY: 74362

Gnomad4 AFR AF: 0.969

Gnomad4 AMR AF: 0.867

Gnomad4 ASJ AF: 0.838

Gnomad4 EAS AF: 0.840

Gnomad4 SAS AF: 0.815

Gnomad4 FIN AF: 0.903

Gnomad4 NFE AF: 0.834

Gnomad4 OTH AF: 0.870

Alfa AF: 0.839 Hom.: 64553

Bravo AF: 0.882

Asia WGS AF: 0.801 AC: 2785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	15
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2399153; hg19: chr22-17493293;