rs1843321

Variant names:

• chr12-30200961-A-G
• rs1843321
• ENST00000549055.1:n.-22A>G

Variant summary

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

The ENST00000549055.1(ENSG00000257262):​n.-22A>G variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 153,274 control chromosomes in the GnomAD database, including 11,897 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 0.32 (11873 hom., cov: 33)
  • Exomes 𝑓: 0.17 (24 hom.)
• Consequence: ENSG00000257262 ENST00000549055.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.121

Genes affected

ENSG00000257262 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 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
ENSG00000257262	ENST00000549055.1	n.-22A>G		upstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48913 AN: 151958 Hom.: 11857 Cov.: 33

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.273

GnomAD4 exome AF: 0.170 AC: 204 AN: 1198 Hom.: 24 Cov.: 0 AF XY: 0.185 AC XY: 122 AN XY: 658

Gnomad4 AFR exome AF: 0.700

Gnomad4 AMR exome AF: 0.167

Gnomad4 ASJ exome AF: 0.107

Gnomad4 EAS exome AF: 0.750

Gnomad4 SAS exome AF: 0.206

Gnomad4 FIN exome AF: 0.182

Gnomad4 NFE exome AF: 0.141

Gnomad4 OTH exome AF: 0.154

GnomAD4 genome AF: 0.322 AC: 48969 AN: 152076 Hom.: 11873 Cov.: 33 AF XY: 0.325 AC XY: 24180 AN XY: 74350

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.272

Alfa AF: 0.215 Hom.: 1084

Bravo AF: 0.334

Asia WGS AF: 0.430 AC: 1495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.5
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1843321; hg19: chr12-30353894;