NM_030768.3:c.532+34A>G

Variant names:

• chr2-238185147-T-C
• rs6431588
• NM_030768.3:c.532+34A>G

Variant summary

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

The NM_030768.3(ILKAP):​c.532+34A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.835 in 1,376,214 control chromosomes in the GnomAD database, including 481,297 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 0.85 (55038 hom., cov: 32)
  • Exomes 𝑓: 0.83 (426259 hom.)
• Consequence: ILKAP NM_030768.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 9 publications found

Genes affected

ILKAP (HGNC:15566): (ILK associated serine/threonine phosphatase) The protein encoded by this gene is a protein serine/threonine phosphatase of the PP2C family. This protein can interact with integrin-linked kinase (ILK/ILK1), a regulator of integrin mediated signaling, and regulate the kinase activity of ILK. Through the interaction with ILK, this protein may selectively affect the signaling process of ILK-mediated glycogen synthase kinase 3 beta (GSK3beta), and thus participate in Wnt signaling pathway. [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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030768.3. 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
	ILKAP	NM_030768.3	MANE Select	c.532+34A>G		intron	N/A	NP_110395.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ILKAP	ENST00000254654.8	TSL:1 MANE Select	c.532+34A>G		intron	N/A	ENSP00000254654.3
	ILKAP	ENST00000622223.4	TSL:1	c.179-1034A>G		intron	N/A	ENSP00000477542.1
	ILKAP	ENST00000612675.4	TSL:1	c.426-1034A>G		intron	N/A	ENSP00000477533.1

Frequencies

GnomAD3 genomes AF: 0.849 AC: 129036 AN: 152044 Hom.: 54976 Cov.: 32

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.873

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.856

GnomAD2 exomes AF: 0.857 AC: 207649 AN: 242268 AF XY: 0.857

Gnomad AFR exome AF: 0.888

Gnomad AMR exome AF: 0.912

Gnomad ASJ exome AF: 0.879

Gnomad EAS exome AF: 0.994

Gnomad FIN exome AF: 0.785

Gnomad NFE exome AF: 0.809

Gnomad OTH exome AF: 0.846

GnomAD4 exome AF: 0.833 AC: 1019608 AN: 1224052 Hom.: 426259 Cov.: 16 AF XY: 0.836 AC XY: 518014 AN XY: 619366

African (AFR) AF: 0.889 AC: 25512 AN: 28696

American (AMR) AF: 0.907 AC: 39746 AN: 43822

Ashkenazi Jewish (ASJ) AF: 0.884 AC: 21812 AN: 24676

East Asian (EAS) AF: 0.994 AC: 38176 AN: 38412

South Asian (SAS) AF: 0.919 AC: 73961 AN: 80494

European-Finnish (FIN) AF: 0.784 AC: 41591 AN: 53066

Middle Eastern (MID) AF: 0.906 AC: 4801 AN: 5298

European-Non Finnish (NFE) AF: 0.813 AC: 729711 AN: 897178

Other (OTH) AF: 0.845 AC: 44298 AN: 52410

GnomAD4 genome AF: 0.849 AC: 129159 AN: 152162 Hom.: 55038 Cov.: 32 AF XY: 0.852 AC XY: 63344 AN XY: 74370

African (AFR) AF: 0.885 AC: 36749 AN: 41510

American (AMR) AF: 0.873 AC: 13344 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.886 AC: 3076 AN: 3470

East Asian (EAS) AF: 0.994 AC: 5152 AN: 5182

South Asian (SAS) AF: 0.909 AC: 4390 AN: 4830

European-Finnish (FIN) AF: 0.797 AC: 8425 AN: 10572

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.812 AC: 55213 AN: 67994

Other (OTH) AF: 0.857 AC: 1811 AN: 2112

Alfa AF: 0.831 Hom.: 122519

Bravo AF: 0.854

Asia WGS AF: 0.934 AC: 3245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.9
DANN	Benign	0.69
PhyloP100		0.34
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs6431588; hg19: chr2-239093788;