rs2399153

Positions:

• 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 22-17012403-A-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: ENST00000605217.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875

Genes affected

(HGNC:):

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000605217.1			upstream_gene_variant

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;