rs4628333

Positions:

• chr9-21238963-G-A
• chr9-21238963-G-C

Variant summary

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

The variant allele was found at a frequency of 0.216 in 151,416 control chromosomes in the GnomAD database, including 3,887 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 0.22 (3878 hom., cov: 32)
  • Exomes 𝑓: 0.18 (9 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

Genes affected

(HGNC:):

IFNA14 (HGNC:5420): (interferon alpha 14) 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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.21238963G>A		intergenic_region
IFNA14	NM_002172.3	c.*403C>T		downstream_gene_variant		ENST00000380222.4	NP_002163.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFNA14	ENST00000380222.4	c.*403C>T		downstream_gene_variant		6	NM_002172.3	ENSP00000369571.2

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32571 AN: 150812 Hom.: 3875 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.154

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.209

GnomAD4 exome AF: 0.183 AC: 89 AN: 486 Hom.: 9 Cov.: 0 AF XY: 0.179 AC XY: 65 AN XY: 364

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.474

Gnomad4 SAS exome AF: 0.0714

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.153

Gnomad4 OTH exome AF: 0.300

GnomAD4 genome AF: 0.216 AC: 32604 AN: 150930 Hom.: 3878 Cov.: 32 AF XY: 0.217 AC XY: 15971 AN XY: 73756

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.209

Alfa AF: 0.161 Hom.: 1377

Bravo AF: 0.225

Asia WGS AF: 0.249 AC: 856 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.25
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4628333; hg19: chr9-21238962;