chr9-21367827-A-T

Variant names:

• chr9-21367827-A-T
• rs766804736
• NM_006900.4:c.184T>A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_006900.4(IFNA13):​c.184T>A​(p.Phe62Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 12/17 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 25)
• Consequence: IFNA13 NM_006900.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.56

Genes affected

IFNA13 (HGNC:5419): (interferon alpha 13) 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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFNA13	NM_006900.4	c.184T>A	p.Phe62Ile	missense_variant	Exon 1 of 1	ENST00000610660.2	NP_008831.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNA13	ENST00000610660.2	c.184T>A	p.Phe62Ile	missense_variant	Exon 1 of 1	6	NM_006900.4	ENSP00000480467.1
IFNA13	ENST00000449498.2	c.181T>A	p.Phe61Ile	missense_variant	Exon 1 of 1	6		ENSP00000394494.2

Frequencies

GnomAD3 genomes Cov.: 25

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 25

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.21
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.40
CADD	Benign	20
DANN	Benign	0.95
Eigen	Benign	-0.63
Eigen_PC	Benign	-0.76
FATHMM_MKL	Benign	0.095	N
LIST_S2	Benign	0.70	.;T
M_CAP	Benign	0.0034	T
MetaRNN	Uncertain	0.42	T;T
MetaSVM	Benign	-1.0	T
PrimateAI	Benign	0.39	T
REVEL	Benign	0.071
Sift4G	Uncertain	0.018	D;D
Vest4		0.51
MutPred		0.73		.;Loss of disorder (P = 0.178);
MVP		0.14
MPC		2.3
ClinPred		0.97	D
GERP RS		2.6
gMVP		0.29

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs766804736; hg19: chr9-21367826;