NM_021002.2:c.*239T>A

Variant names:

• chr9-21350079-A-T
• rs2990144
• NM_021002.2:c.*239T>A

Variant summary

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

The NM_021002.2(IFNA6):​c.*239T>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 228,022 control chromosomes in the GnomAD database, including 4,071 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 0.18 (2611 hom., cov: 32)
  • Exomes 𝑓: 0.19 (1460 hom.)
• Consequence: IFNA6 NM_021002.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.663
• Publications: 2 publications found

Genes affected

IFNA6 (HGNC:5427): (interferon alpha 6) 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. Biomarker of anogenital venereal wart. [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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021002.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNA6	NM_021002.2	MANE Select	c.*239T>A		downstream_gene	N/A	NP_066282.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNA6	ENST00000380210.2	TSL:6 MANE Select	c.*239T>A		downstream_gene	N/A	ENSP00000369558.1
	IFNA6	ENST00000259555.5	TSL:6	c.*239T>A		downstream_gene	N/A	ENSP00000259555.5

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27411 AN: 152102 Hom.: 2609 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.181

GnomAD4 exome AF: 0.187 AC: 14171 AN: 75802 Hom.: 1460 Cov.: 2 AF XY: 0.186 AC XY: 7280 AN XY: 39198

African (AFR) AF: 0.184 AC: 365 AN: 1984

American (AMR) AF: 0.247 AC: 949 AN: 3848

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 505 AN: 2580

East Asian (EAS) AF: 0.308 AC: 1602 AN: 5194

South Asian (SAS) AF: 0.119 AC: 331 AN: 2788

European-Finnish (FIN) AF: 0.197 AC: 1048 AN: 5326

Middle Eastern (MID) AF: 0.148 AC: 55 AN: 372

European-Non Finnish (NFE) AF: 0.172 AC: 8376 AN: 48832

Other (OTH) AF: 0.193 AC: 940 AN: 4878

GnomAD4 genome AF: 0.180 AC: 27428 AN: 152220 Hom.: 2611 Cov.: 32 AF XY: 0.182 AC XY: 13548 AN XY: 74426

African (AFR) AF: 0.168 AC: 6980 AN: 41536

American (AMR) AF: 0.241 AC: 3691 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 703 AN: 3468

East Asian (EAS) AF: 0.304 AC: 1580 AN: 5190

South Asian (SAS) AF: 0.110 AC: 528 AN: 4820

European-Finnish (FIN) AF: 0.191 AC: 2022 AN: 10596

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11362 AN: 68008

Other (OTH) AF: 0.181 AC: 383 AN: 2112

Alfa AF: 0.0986 Hom.: 143

Bravo AF: 0.186

Asia WGS AF: 0.189 AC: 656 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.0
DANN	Benign	0.77
PhyloP100		0.66
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2990144; hg19: chr9-21350078;