chr11-68089043-C-A

Variant names:

• chr11-68089043-C-A
• rs2511437
• NM_001277.3:c.463-7586G>T

Variant summary

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

The NM_001277.3(CHKA):​c.463-7586G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 152,092 control chromosomes in the GnomAD database, including 28,833 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 0.62 (28833 hom., cov: 32)
• Consequence: CHKA NM_001277.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 9 publications found

Genes affected

CHKA (HGNC:1937): (choline kinase alpha) The major pathway for the biosynthesis of phosphatidylcholine occurs via the CDP-choline pathway. The protein encoded by this gene is the initial enzyme in the sequence and may play a regulatory role. The encoded protein also catalyzes the phosphorylation of ethanolamine. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

CHKA Gene-Disease associations (from GenCC):

• neurodevelopmental disorder with microcephaly, movement abnormalities, and seizures

  Inheritance: AR Classification: STRONG, MODERATE, LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001277.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHKA	NM_001277.3	MANE Select	c.463-7586G>T		intron	N/A	NP_001268.2
	CHKA	NM_001376219.1		c.463-6523G>T		intron	N/A	NP_001363148.1
	CHKA	NM_212469.2		c.462+7976G>T		intron	N/A	NP_997634.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHKA	ENST00000265689.9	TSL:1 MANE Select	c.463-7586G>T		intron	N/A	ENSP00000265689.4
	CHKA	ENST00000356135.9	TSL:1	c.462+7976G>T		intron	N/A	ENSP00000348454.4
	CHKA	ENST00000931669.1		c.463-7586G>T		intron	N/A	ENSP00000601728.1

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93477 AN: 151974 Hom.: 28800 Cov.: 32

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.742

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.637

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

GnomAD4 genome AF: 0.615 AC: 93568 AN: 152092 Hom.: 28833 Cov.: 32 AF XY: 0.618 AC XY: 45941 AN XY: 74340

African (AFR) AF: 0.600 AC: 24899 AN: 41478

American (AMR) AF: 0.681 AC: 10419 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2360 AN: 3472

East Asian (EAS) AF: 0.651 AC: 3370 AN: 5178

South Asian (SAS) AF: 0.728 AC: 3511 AN: 4822

European-Finnish (FIN) AF: 0.587 AC: 6200 AN: 10556

Middle Eastern (MID) AF: 0.747 AC: 218 AN: 292

European-Non Finnish (NFE) AF: 0.599 AC: 40700 AN: 67980

Other (OTH) AF: 0.639 AC: 1349 AN: 2112

Alfa AF: 0.613 Hom.: 46827

Bravo AF: 0.624

Asia WGS AF: 0.670 AC: 2333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.94
DANN	Benign	0.51
PhyloP100		-0.075
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: rs2511437; hg19: chr11-67856510;