NM_030768.3:c.425+1350C>T

Variant names:

• chr2-238186781-G-A
• rs12472274
• NM_030768.3:c.425+1350C>T

Variant summary

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

The NM_030768.3(ILKAP):​c.425+1350C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 150,978 control chromosomes in the GnomAD database, including 4,357 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 0.23 (4357 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ILKAP NM_030768.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230
• Publications: 17 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ILKAP	NM_030768.3	c.425+1350C>T		intron_variant	Intron 5 of 11	ENST00000254654.8	NP_110395.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ILKAP	ENST00000254654.8	c.425+1350C>T		intron_variant	Intron 5 of 11	1	NM_030768.3	ENSP00000254654.3

Frequencies

GnomAD3 genomes AF: 0.231 AC: 34906 AN: 150892 Hom.: 4348 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.238

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.231 AC: 34951 AN: 150978 Hom.: 4357 Cov.: 32 AF XY: 0.235 AC XY: 17313 AN XY: 73664

African (AFR) AF: 0.187 AC: 7702 AN: 41132

American (AMR) AF: 0.316 AC: 4794 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1028 AN: 3458

East Asian (EAS) AF: 0.480 AC: 2473 AN: 5154

South Asian (SAS) AF: 0.258 AC: 1237 AN: 4800

European-Finnish (FIN) AF: 0.215 AC: 2172 AN: 10124

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.219 AC: 14825 AN: 67824

Other (OTH) AF: 0.238 AC: 501 AN: 2102

Alfa AF: 0.230 Hom.: 18589

Bravo AF: 0.235

Asia WGS AF: 0.315 AC: 1094 AN: 3478

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	0.44
PhyloP100		-0.023
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: rs12472274; hg19: chr2-239095422;