rs10791957

Variant names:

• chr11-68100081-C-A
• rs10791957
• NM_001277.3:c.351-2951G>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CHKA	NM_001277.3	c.351-2951G>T		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.351-2951G>T		intron_variant	Intron 1 of 11	1	NM_001277.3	ENSP00000265689.4
CHKA	ENST00000356135.9	c.351-2951G>T		intron_variant	Intron 1 of 10	1		ENSP00000348454.4
CHKA	ENST00000531341.1	c.-16-2951G>T		intron_variant	Intron 1 of 5	3		ENSP00000435032.1

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

African (AFR) AF: 0.397 AC: 16458 AN: 41462

American (AMR) AF: 0.645 AC: 9834 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2125 AN: 3470

East Asian (EAS) AF: 0.635 AC: 3279 AN: 5166

South Asian (SAS) AF: 0.685 AC: 3309 AN: 4828

European-Finnish (FIN) AF: 0.586 AC: 6182 AN: 10544

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38066 AN: 67984

Other (OTH) AF: 0.567 AC: 1197 AN: 2110

Alfa AF: 0.564 Hom.: 97750

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
PhyloP100		-1.3
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

Publications

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Other links and lift over

dbSNP: rs10791957; hg19: chr11-67867548;