rs4930557

chr11-68110690-C-T

Variant summary

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

The NM_001277.3(CHKA):c.350+10138G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 151,880 control chromosomes in the GnomAD database, including 24,746 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 0.57 (24746 hom., cov: 31)
• Consequence: CHKA NM_001277.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.105

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]

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 (SAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHKA	NM_001277.3	c.350+10138G>A		intron_variant		ENST00000265689.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHKA	ENST00000265689.9	c.350+10138G>A		intron_variant		1	NM_001277.3
CHKA	ENST00000356135.9	c.350+10138G>A		intron_variant		1		P1
CHKA	ENST00000531341.1	c.-17+10100G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86439 AN: 151762 Hom.: 24735 Cov.: 31

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.569 AC: 86489 AN: 151880 Hom.: 24746 Cov.: 31 AF XY: 0.574 AC XY: 42625 AN XY: 74216

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.686

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.591

Alfa AF: 0.564 Hom.: 3543

Bravo AF: 0.577

Asia WGS AF: 0.630 AC: 2192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	8.9
Dann	Benign	0.93

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: rs4930557; hg19: chr11-67878157;