rs11481
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
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
NM_001277.3 3_prime_UTR
Scores
2
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
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 | UniProt |
---|---|---|---|---|---|---|---|
CHKA | NM_001277.3 | c.*1120A>T | 3_prime_UTR_variant | 12/12 | ENST00000265689.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHKA | ENST00000265689.9 | c.*1120A>T | 3_prime_UTR_variant | 12/12 | 1 | NM_001277.3 | |||
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: 92690AN: 151950Hom.: 29595 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
92690
AN:
151950
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.672 AC: 39AN: 58Hom.: 13 Cov.: 0 AF XY: 0.643 AC XY: 18AN XY: 28
GnomAD4 exome
AF:
AC:
39
AN:
58
Hom.:
Cov.:
0
AF XY:
AC XY:
18
AN XY:
28
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.610 AC: 92736AN: 152068Hom.: 29607 Cov.: 32 AF XY: 0.617 AC XY: 45821AN XY: 74320
GnomAD4 genome
?
AF:
AC:
92736
AN:
152068
Hom.:
Cov.:
32
AF XY:
AC XY:
45821
AN XY:
74320
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2411
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at