rs11481

Positions:

• chr11-68052868-T-A
• chr11-68052868-T-G

Variant summary

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

The NM_001277.3(CHKA):​c.*1120A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 152,126 control chromosomes in the GnomAD database, including 29,620 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 0.61 (29607 hom., cov: 32)
  • Exomes 𝑓: 0.67 (13 hom.)
• Consequence: CHKA NM_001277.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.733 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHKA	NM_001277.3	c.*1120A>T		3_prime_UTR_variant	12/12	ENST00000265689.9	NP_001268.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHKA	ENST00000265689.9	c.*1120A>T		3_prime_UTR_variant	12/12	1	NM_001277.3	ENSP00000265689
	ENST00000529934.5	n.194-112T>A		intron_variant, non_coding_transcript_variant		5
	ENST00000534517.1	n.46T>A		non_coding_transcript_exon_variant	1/2	2
	ENST00000526897.1	n.350-112T>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92690 AN: 151950 Hom.: 29595 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.665

GnomAD4 exome AF: 0.672 AC: 39 AN: 58 Hom.: 13 Cov.: 0 AF XY: 0.643 AC XY: 18 AN XY: 28

Gnomad4 FIN exome AF: 0.685

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.610 AC: 92736 AN: 152068 Hom.: 29607 Cov.: 32 AF XY: 0.617 AC XY: 45821 AN XY: 74320

Gnomad4 AFR AF: 0.405

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.787

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.686

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.666

Alfa AF: 0.634 Hom.: 3870

Bravo AF: 0.607

Asia WGS AF: 0.694 AC: 2411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	5.1
DANN	Benign	0.88

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: rs11481; hg19: chr11-67820335;