chr9-21228286-A-G

Variant names:

• chr9-21228286-A-G
• rs10964918
• NM_021268.2:c.-113T>C

Variant summary

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

The NM_021268.2(IFNA17):​c.-113T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 1,423,496 control chromosomes in the GnomAD database, including 23,438 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 0.19 (3125 hom., cov: 32)
  • Exomes 𝑓: 0.17 (20313 hom.)
• Consequence: IFNA17 NM_021268.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.96

Genes affected

IFNA17 (HGNC:5422): (interferon alpha 17) Predicted to enable cytokine activity and type I interferon receptor binding activity. Predicted to be involved in several processes, including B cell activation; lymphocyte activation involved in immune response; and positive regulation of peptidyl-serine phosphorylation of STAT protein. Predicted to be located in extracellular region. Predicted to be active in extracellular space. Implicated in Crimean-Congo hemorrhagic fever and sarcoidosis. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFNA17	NM_021268.2	c.-113T>C		upstream_gene_variant		ENST00000413767.2	NP_067091.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNA17	ENST00000413767.2	c.-113T>C		upstream_gene_variant		6	NM_021268.2	ENSP00000411940.2

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29511 AN: 151886 Hom.: 3123 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.193

GnomAD4 exome AF: 0.170 AC: 216102 AN: 1271494 Hom.: 20313 AF XY: 0.168 AC XY: 104282 AN XY: 619586

Gnomad4 AFR exome AF: 0.198

Gnomad4 AMR exome AF: 0.260

Gnomad4 ASJ exome AF: 0.190

Gnomad4 EAS exome AF: 0.432

Gnomad4 SAS exome AF: 0.110

Gnomad4 FIN exome AF: 0.180

Gnomad4 NFE exome AF: 0.160

Gnomad4 OTH exome AF: 0.176

GnomAD4 genome AF: 0.194 AC: 29537 AN: 152002 Hom.: 3125 Cov.: 32 AF XY: 0.195 AC XY: 14498 AN XY: 74290

Gnomad4 AFR AF: 0.202

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.193

Alfa AF: 0.186 Hom.: 330

Bravo AF: 0.202

Asia WGS AF: 0.249 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.048
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10964918; hg19: chr9-21228285;