chr11-68117272-A-T

Variant names:

• chr11-68117272-A-T
• rs6591331
• NM_001277.3:c.350+3556T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001277.3(CHKA):​c.350+3556T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 151,982 control chromosomes in the GnomAD database, including 31,664 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 0.64 (31664 hom., cov: 32)
• Consequence: CHKA NM_001277.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160
• Publications: 7 publications found

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]

CHKA Gene-Disease associations (from GenCC):

• neurodevelopmental disorder with microcephaly, movement abnormalities, and seizures

  Inheritance: AR Classification: STRONG, MODERATE, LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHKA	NM_001277.3	c.350+3556T>A		intron_variant	Intron 1 of 11	ENST00000265689.9	NP_001268.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHKA	ENST00000265689.9	c.350+3556T>A		intron_variant	Intron 1 of 11	1	NM_001277.3	ENSP00000265689.4
CHKA	ENST00000356135.9	c.350+3556T>A		intron_variant	Intron 1 of 10	1		ENSP00000348454.4
CHKA	ENST00000531341.1	c.-17+3518T>A		intron_variant	Intron 1 of 5	3		ENSP00000435032.1

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97744 AN: 151864 Hom.: 31625 Cov.: 32

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.615

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.644 AC: 97841 AN: 151982 Hom.: 31664 Cov.: 32 AF XY: 0.647 AC XY: 48038 AN XY: 74262

African (AFR) AF: 0.687 AC: 28465 AN: 41422

American (AMR) AF: 0.695 AC: 10598 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2381 AN: 3470

East Asian (EAS) AF: 0.653 AC: 3378 AN: 5172

South Asian (SAS) AF: 0.731 AC: 3520 AN: 4814

European-Finnish (FIN) AF: 0.615 AC: 6495 AN: 10554

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40858 AN: 67982

Other (OTH) AF: 0.655 AC: 1384 AN: 2112

Alfa AF: 0.631 Hom.: 3816

Bravo AF: 0.655

Asia WGS AF: 0.691 AC: 2405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	12
DANN	Benign	0.93
PhyloP100		0.016
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6591331; hg19: chr11-67884739;