chr5-140655259-C-T

Variant names:

• chr5-140655259-C-T
• rs801399
• NM_006083.4:c.637+532C>T

Variant summary

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

The NM_006083.4(IK):​c.637+532C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 151,992 control chromosomes in the GnomAD database, including 20,102 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 0.51 (20102 hom., cov: 32)
• Consequence: IK NM_006083.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250
• Publications: 28 publications found

Genes affected

IK (HGNC:5958): (IK cytokine) The protein encoded by this gene was identified by its RED repeat, a stretch of repeated arginine, glutamic acid and aspartic acid residues. The protein localizes to discrete dots within the nucleus, excluding the nucleolus. Its function is unknown. This gene maps to chromosome 5; however, a pseudogene may exist on chromosome 2. [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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006083.4. 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
	IK	NM_006083.4	MANE Select	c.637+532C>T		intron	N/A	NP_006074.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IK	ENST00000417647.7	TSL:1 MANE Select	c.637+532C>T		intron	N/A	ENSP00000396301.2
	IK	ENST00000947150.1		c.627+542C>T		intron	N/A	ENSP00000617209.1
	IK	ENST00000508301.5	TSL:2	c.637+532C>T		intron	N/A	ENSP00000422641.1

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76900 AN: 151874 Hom.: 20060 Cov.: 32

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.487

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.507 AC: 76993 AN: 151992 Hom.: 20102 Cov.: 32 AF XY: 0.509 AC XY: 37801 AN XY: 74298

African (AFR) AF: 0.629 AC: 26056 AN: 41454

American (AMR) AF: 0.465 AC: 7108 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1583 AN: 3472

East Asian (EAS) AF: 0.464 AC: 2396 AN: 5164

South Asian (SAS) AF: 0.435 AC: 2100 AN: 4824

European-Finnish (FIN) AF: 0.550 AC: 5798 AN: 10542

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30627 AN: 67952

Other (OTH) AF: 0.491 AC: 1035 AN: 2108

Alfa AF: 0.480 Hom.: 3684

Bravo AF: 0.502

Asia WGS AF: 0.533 AC: 1852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.60
PhyloP100		-0.025
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: rs801399; hg19: chr5-140034844;