chr2-238185147-T-C

Position:

• chr2-238185147-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ILKAP	NM_030768.3	c.532+34A>G		intron_variant		ENST00000254654.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ILKAP	ENST00000254654.8	c.532+34A>G		intron_variant		1	NM_030768.3	P1

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

GnomAD3 exomes AF: 0.857 AC: 207649 AN: 242268 Hom.: 89443 AF XY: 0.857 AC XY: 112244 AN XY: 130918

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 SAS exome AF: 0.919

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

Gnomad4 AFR exome AF: 0.889

Gnomad4 AMR exome AF: 0.907

Gnomad4 ASJ exome AF: 0.884

Gnomad4 EAS exome AF: 0.994

Gnomad4 SAS exome AF: 0.919

Gnomad4 FIN exome AF: 0.784

Gnomad4 NFE exome AF: 0.813

Gnomad4 OTH exome AF: 0.845

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

Gnomad4 AFR AF: 0.885

Gnomad4 AMR AF: 0.873

Gnomad4 ASJ AF: 0.886

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.909

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.812

Gnomad4 OTH AF: 0.857

Alfa AF: 0.826 Hom.: 92435

Bravo AF: 0.854

Asia WGS AF: 0.934 AC: 3245 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.9
DANN	Benign	0.69
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

Publications

LitVar

Other links and lift over

dbSNP: rs6431588; hg19: chr2-239093788;