Variant rs231247 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_025144.4(ALPK1):c.3252A>G(p.Arg1084=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 1,613,226 control chromosomes in the GnomAD database, including 350,441 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.68 ( 35554 hom., cov: 31)

Exomes 𝑓: 0.65 ( 314887 hom. )

Consequence

ALPK1
NM_025144.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.417

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP6

Variant 4-112438547-A-G is Benign according to our data. Variant chr4-112438547-A-G is described in ClinVar as [Benign]. Clinvar id is 2115848.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.417 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
ALPK1	NM_025144.4 linkuse as main transcript	c.3252A>G	p.Arg1084=	synonymous_variant	13/16	ENST00000650871.1
ALPK1	NM_001102406.2 linkuse as main transcript	c.3252A>G	p.Arg1084=	synonymous_variant	13/16
ALPK1	NM_001253884.2 linkuse as main transcript	c.3018A>G	p.Arg1006=	synonymous_variant	12/15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ALPK1	ENST00000650871.1 linkuse as main transcript	c.3252A>G	p.Arg1084=	synonymous_variant	13/16		NM_025144.4	P1	Q96QP1-1

Frequencies

GnomAD3 genomes

AF:

0.682

AC:

103652

AN:

151882

Hom.:

35531

Cov.:

show subpopulations

Gnomad AFR

AF:

0.734

Gnomad AMI

AF:

0.763

Gnomad AMR

AF:

0.619

Gnomad ASJ

AF:

0.707

Gnomad EAS

AF:

0.718

Gnomad SAS

AF:

0.579

Gnomad FIN

AF:

0.717

Gnomad MID

AF:

0.627

Gnomad NFE

AF:

0.662

Gnomad OTH

AF:

0.682

GnomAD3 exomes

AF:

0.650

AC:

163265

AN:

251078

Hom.:

53652

AF XY:

0.648

AC XY:

87888

AN XY:

135692

show subpopulations

Gnomad AFR exome

AF:

0.732

Gnomad AMR exome

AF:

0.561

Gnomad ASJ exome

AF:

0.709

Gnomad EAS exome

AF:

0.712

Gnomad SAS exome

AF:

0.573

Gnomad FIN exome

AF:

0.706

Gnomad NFE exome

AF:

0.660

Gnomad OTH exome

AF:

0.654

GnomAD4 exome

AF:

0.655

AC:

957012

AN:

1461226

Hom.:

314887

Cov.:

AF XY:

0.653

AC XY:

474698

AN XY:

726918

show subpopulations

Gnomad4 AFR exome

AF:

0.736

Gnomad4 AMR exome

AF:

0.571

Gnomad4 ASJ exome

AF:

0.712

Gnomad4 EAS exome

AF:

0.727

Gnomad4 SAS exome

AF:

0.576

Gnomad4 FIN exome

AF:

0.703

Gnomad4 NFE exome

AF:

0.656

Gnomad4 OTH exome

AF:

0.661

GnomAD4 genome

AF:

0.682

AC:

103728

AN:

152000

Hom.:

35554

Cov.:

AF XY:

0.682

AC XY:

50691

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.734

Gnomad4 AMR

AF:

0.619

Gnomad4 ASJ

AF:

0.707

Gnomad4 EAS

AF:

0.718

Gnomad4 SAS

AF:

0.577

Gnomad4 FIN

AF:

0.717

Gnomad4 NFE

AF:

0.662

Gnomad4 OTH

AF:

0.681

Alfa

AF:

0.661

Hom.:

53322

Bravo

AF:

0.679

Asia WGS

AF:

0.585

AC:

2039

AN:

3478

EpiCase

AF:

0.663

EpiControl

AF:

0.654

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

6.7

DANN

Benign

0.64

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over