rs4628333

Variant names:

• chr9-21238963-G-A
• rs4628333
• NM_002172.3:c.*403C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The NM_002172.3(IFNA14):​c.*403C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. 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: IFNA14 NM_002172.3 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 2 publications found

Genes affected

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
IFNA14	NM_002172.3	c.*403C>T		downstream_gene_variant		ENST00000380222.4	NP_002163.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AF: 0.250 AC: 2 AN: 8

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6

East Asian (EAS) AF: 0.474 AC: 18 AN: 38

South Asian (SAS) AF: 0.0714 AC: 1 AN: 14

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.153 AC: 60 AN: 392

Other (OTH) AF: 0.300 AC: 6 AN: 20

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

African (AFR) AF: 0.275 AC: 11385 AN: 41346

American (AMR) AF: 0.255 AC: 3860 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 694 AN: 3446

East Asian (EAS) AF: 0.400 AC: 2061 AN: 5154

South Asian (SAS) AF: 0.113 AC: 543 AN: 4800

European-Finnish (FIN) AF: 0.194 AC: 1997 AN: 10274

Middle Eastern (MID) AF: 0.153 AC: 44 AN: 288

European-Non Finnish (NFE) AF: 0.170 AC: 11445 AN: 67484

Other (OTH) AF: 0.209 AC: 437 AN: 2086

Alfa AF: 0.165 Hom.: 1656

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4628333; hg19: chr9-21238962;