9-21217536-C-G

Variant names:

• chr9-21217536-C-G
• rs1834247
• NM_002173.3:c.-231G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002173.3(IFNA16):​c.-231G>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 151,992 control chromosomes in the GnomAD database, including 3,127 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 (3127 hom., cov: 32)
• Consequence: IFNA16 NM_002173.3 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18
• Publications: 3 publications found

Genes affected

IFNA16 (HGNC:5421): (interferon alpha 16) 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. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFNA16	NM_002173.3	c.-231G>C		upstream_gene_variant		ENST00000380216.1	NP_002164.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNA16	ENST00000380216.1	c.-231G>C		upstream_gene_variant		6	NM_002173.3	ENSP00000369564.1

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29511 AN: 151874 Hom.: 3124 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.193

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.194 AC: 29538 AN: 151992 Hom.: 3127 Cov.: 32 AF XY: 0.195 AC XY: 14492 AN XY: 74286

African (AFR) AF: 0.202 AC: 8358 AN: 41466

American (AMR) AF: 0.245 AC: 3733 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 692 AN: 3472

East Asian (EAS) AF: 0.412 AC: 2128 AN: 5168

South Asian (SAS) AF: 0.113 AC: 544 AN: 4814

European-Finnish (FIN) AF: 0.191 AC: 2012 AN: 10554

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11482 AN: 67954

Other (OTH) AF: 0.193 AC: 406 AN: 2100

Alfa AF: 0.0919 Hom.: 139

Bravo AF: 0.201

Asia WGS AF: 0.249 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.064
DANN	Benign	0.44
PhyloP100		-2.2
PromoterAI		-0.0088	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1834247; hg19: chr9-21217535;