rs10791957

Positions:

• chr11-68100081-C-A
• chr11-68100081-C-G

Variant summary

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

The NM_001277.3(CHKA):​c.351-2951G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 152,022 control chromosomes in the GnomAD database, including 22,229 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 0.53 (22229 hom., cov: 33)
• Consequence: CHKA NM_001277.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

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=-0.88).
• 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.351-2951G>T		intron_variant		ENST00000265689.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHKA	ENST00000265689.9	c.351-2951G>T		intron_variant		1	NM_001277.3
CHKA	ENST00000356135.9	c.351-2951G>T		intron_variant		1		P1
CHKA	ENST00000531341.1	c.-16-2951G>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81089 AN: 151904 Hom.: 22221 Cov.: 33

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.534 AC: 81114 AN: 152022 Hom.: 22229 Cov.: 33 AF XY: 0.539 AC XY: 40071 AN XY: 74282

Gnomad4 AFR AF: 0.397

Gnomad4 AMR AF: 0.645

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.635

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.567

Alfa AF: 0.573 Hom.: 53388

Bravo AF: 0.536

Asia WGS AF: 0.617 AC: 2144 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.34
DANN	Benign	0.27

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: rs10791957; hg19: chr11-67867548;