chr9-27526049-C-T

Variant names:

• chr9-27526049-C-T
• rs700782
• NM_020124.3:c.*44C>T

Variant summary

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

The NM_020124.3(IFNK):​c.*44C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 151,924 control chromosomes in the GnomAD database, including 4,683 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 0.24 (4683 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: IFNK NM_020124.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 16 publications found

Genes affected

IFNK (HGNC:21714): (interferon kappa) This gene encodes a member of the type I interferon family. Type I interferons are a group of related glycoproteins that play an important role in host defenses against viral infections. This protein is expressed in keratinocytes and the gene is found on chromosome 9, adjacent to the type I interferon cluster. [provided by RefSeq, Jul 2008]

MOB3B (HGNC:23825): (MOB kinase activator 3B) The protein encoded by this gene shares similarity with the yeast Mob1 protein. Yeast Mob1 binds Mps1p, a protein kinase essential for spindle pole body duplication and mitotic checkpoint regulation. This gene is located on the opposite strand as the interferon kappa precursor (IFNK) gene. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020124.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNK	NM_020124.3	MANE Select	c.*44C>T		3_prime_UTR	Exon 2 of 2	NP_064509.2	Q9P0W0
	MOB3B	NM_024761.5	MANE Select	c.-199+3506G>A		intron	N/A	NP_079037.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFNK	ENST00000276943.3	TSL:1 MANE Select	c.*44C>T		3_prime_UTR	Exon 2 of 2	ENSP00000276943.2	Q9P0W0
	MOB3B	ENST00000262244.6	TSL:1 MANE Select	c.-199+3506G>A		intron	N/A	ENSP00000262244.5	Q86TA1
	MOB3B	ENST00000900190.1		c.-199+3506G>A		intron	N/A	ENSP00000570249.1

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37082 AN: 151802 Hom.: 4672 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.252

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.244 AC: 37120 AN: 151920 Hom.: 4683 Cov.: 32 AF XY: 0.246 AC XY: 18219 AN XY: 74202

African (AFR) AF: 0.230 AC: 9541 AN: 41442

American (AMR) AF: 0.302 AC: 4614 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 736 AN: 3470

East Asian (EAS) AF: 0.291 AC: 1500 AN: 5160

South Asian (SAS) AF: 0.280 AC: 1349 AN: 4810

European-Finnish (FIN) AF: 0.183 AC: 1913 AN: 10460

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16608 AN: 67982

Other (OTH) AF: 0.249 AC: 526 AN: 2110

Alfa AF: 0.250 Hom.: 8721

Bravo AF: 0.254

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.9
DANN	Benign	0.71
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs700782; hg19: chr9-27526047;