chr11-68077412-C-T

Position:

• chr11-68077412-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.517-2582G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 151,898 control chromosomes in the GnomAD database, including 24,443 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 (24443 hom., cov: 31)
• Consequence: CHKA NM_001277.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

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=-0.96).
• 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	Protein	UniProt
CHKA	NM_001277.3	c.517-2582G>A		intron_variant		ENST00000265689.9	NP_001268.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHKA	ENST00000265689.9	c.517-2582G>A		intron_variant		1	NM_001277.3	ENSP00000265689

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85858 AN: 151778 Hom.: 24429 Cov.: 31

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.701

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.566 AC: 85913 AN: 151898 Hom.: 24443 Cov.: 31 AF XY: 0.571 AC XY: 42377 AN XY: 74262

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.658

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.635

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.589

Alfa AF: 0.564 Hom.: 5438

Bravo AF: 0.573

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	-0.96
CADD	Benign	0.051
DANN	Benign	0.30

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: rs2512612; hg19: chr11-67844879;