chr4-112386555-C-G

Position:

• chr4-112386555-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_025144.4(ALPK1):​c.276+4003C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.892 in 152,220 control chromosomes in the GnomAD database, including 60,790 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 0.89 (60790 hom., cov: 31)
• Consequence: ALPK1 NM_025144.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.50

Genes affected

ALPK1 (HGNC:20917): (alpha kinase 1) This gene encodes an alpha kinase. Mice which were homozygous for disrupted copies of this gene exhibited coordination defects (PMID: 21208416). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

ALPK1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ALPK1	NM_025144.4	c.276+4003C>G		intron_variant		ENST00000650871.1	NP_079420.3
ALPK1	NM_001102406.2	c.276+4003C>G		intron_variant			NP_001095876.1
ALPK1	NM_001253884.2	c.42+8657C>G		intron_variant			NP_001240813.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALPK1	ENST00000650871.1	c.276+4003C>G		intron_variant			NM_025144.4	ENSP00000498374.1

Frequencies

GnomAD3 genomes AF: 0.892 AC: 135631 AN: 152102 Hom.: 60728 Cov.: 31

Gnomad AFR AF: 0.974

Gnomad AMI AF: 0.850

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.931

Gnomad EAS AF: 0.883

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.914

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

GnomAD4 genome AF: 0.892 AC: 135754 AN: 152220 Hom.: 60790 Cov.: 31 AF XY: 0.893 AC XY: 66432 AN XY: 74426

Gnomad4 AFR AF: 0.974

Gnomad4 AMR AF: 0.903

Gnomad4 ASJ AF: 0.931

Gnomad4 EAS AF: 0.883

Gnomad4 SAS AF: 0.743

Gnomad4 FIN AF: 0.873

Gnomad4 NFE AF: 0.851

Gnomad4 OTH AF: 0.915

Alfa AF: 0.830 Hom.: 2519

Bravo AF: 0.903

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	16
DANN	Benign	0.70

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: rs2051778; hg19: chr4-113307711;