9-27526049-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFNK	NM_020124.3	c.*44C>T		3_prime_UTR_variant	Exon 2 of 2	ENST00000276943.3	NP_064509.2
MOB3B	NM_024761.5	c.-199+3506G>A		intron_variant	Intron 1 of 3	ENST00000262244.6	NP_079037.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNK	ENST00000276943.3	c.*44C>T		3_prime_UTR_variant	Exon 2 of 2	1	NM_020124.3	ENSP00000276943.2
MOB3B	ENST00000262244.6	c.-199+3506G>A		intron_variant	Intron 1 of 3	1	NM_024761.5	ENSP00000262244.5

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

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.00

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

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.249

Alfa AF: 0.251 Hom.: 6322

Bravo AF: 0.254

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.9
DANN	Benign	0.71

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

Publications

LitVar

Other links and lift over

dbSNP: rs700782; hg19: chr9-27526047;