rs2511437

chr11-68089043-C-Achr11-68089043-C-Gchr11-68089043-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.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

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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHKA	NM_001277.3	c.463-7586G>T		intron_variant		ENST00000265689.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHKA	ENST00000265689.9	c.463-7586G>T		intron_variant		1	NM_001277.3
CHKA	ENST00000356135.9	c.462+7976G>T		intron_variant		1		P1
CHKA	ENST00000531341.1	c.97-7586G>T		intron_variant		3
CHKA	ENST00000528235.5	n.60+778G>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.600

Gnomad4 AMR AF: 0.681

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.728

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.639

Alfa AF: 0.611 Hom.: 36375

Bravo AF: 0.624

Asia WGS AF: 0.670 AC: 2333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.94
Dann	Benign	0.51

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: rs2511437; hg19: chr11-67856510;