4-112287558-A-G

Position:

• chr4-112287558-A-G

Variant summary

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

The ENST00000514594.1(ALPK1):​n.253+1797A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0329 in 152,298 control chromosomes in the GnomAD database, including 170 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 0.033 (170 hom., cov: 32)
• Consequence: ALPK1 ENST00000514594.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.568

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ALPK1	ENST00000514594.1	n.253+1797A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0329 AC: 5001 AN: 152180 Hom.: 166 Cov.: 32

Gnomad AFR AF: 0.0742

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0239

Gnomad ASJ AF: 0.0381

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.00725

Gnomad FIN AF: 0.0155

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.00466

Gnomad OTH AF: 0.0411

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

GnomAD4 genome AF: 0.0329 AC: 5015 AN: 152298 Hom.: 170 Cov.: 32 AF XY: 0.0335 AC XY: 2497 AN XY: 74482

Gnomad4 AFR AF: 0.0745

Gnomad4 AMR AF: 0.0238

Gnomad4 ASJ AF: 0.0381

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.00705

Gnomad4 FIN AF: 0.0155

Gnomad4 NFE AF: 0.00466

Gnomad4 OTH AF: 0.0402

Alfa AF: 0.00890 Hom.: 5

Bravo AF: 0.0373

Asia WGS AF: 0.0810 AC: 281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.5
DANN	Benign	0.56

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7668738; hg19: chr4-113208714;