rs16949816

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014772.3(CTIF):​c.508-15623G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0941 in 152,252 control chromosomes in the GnomAD database, including 1,896 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 0.094 ( 1896 hom., cov: 33)

Consequence

CTIF
NM_014772.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.541
Variant links:
Genes affected
CTIF (HGNC:23925): (cap binding complex dependent translation initiation factor) CTIF is a component of the CBP80 (NCBP1; MIM 600469)/CBP20 (NCBP2; MIM 605133) translation initiation complex that binds cotranscriptionally to the cap end of nascent mRNA. The CBP80/CBP20 complex is involved in a simultaneous editing and translation step that recognizes premature termination codons (PTCs) in mRNAs and directs PTC-containing mRNAs toward nonsense-mediated decay (NMD). On mRNAs without PTCs, the CBP80/CBP20 complex is replaced with cytoplasmic mRNA cap-binding proteins, including EIF4G (MIM 600495), and steady-state translation of the mRNAs resumes in the cytoplasm (Kim et al., 2009 [PubMed 19648179]).[supplied by OMIM, Dec 2009]

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=-0.84).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CTIFNM_014772.3 linkuse as main transcriptc.508-15623G>A intron_variant ENST00000256413.8
LOC105372107XR_007066460.1 linkuse as main transcriptn.8430C>T non_coding_transcript_exon_variant 1/4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CTIFENST00000256413.8 linkuse as main transcriptc.508-15623G>A intron_variant 1 NM_014772.3 A1O43310-1

Frequencies

GnomAD3 genomes
AF:
0.0940
AC:
14307
AN:
152134
Hom.:
1894
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.298
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0446
Gnomad ASJ
AF:
0.0680
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00641
Gnomad FIN
AF:
0.0106
Gnomad MID
AF:
0.0601
Gnomad NFE
AF:
0.0108
Gnomad OTH
AF:
0.0683
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0941
AC:
14330
AN:
152252
Hom.:
1896
Cov.:
33
AF XY:
0.0914
AC XY:
6808
AN XY:
74454
show subpopulations
Gnomad4 AFR
AF:
0.298
Gnomad4 AMR
AF:
0.0446
Gnomad4 ASJ
AF:
0.0680
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00663
Gnomad4 FIN
AF:
0.0106
Gnomad4 NFE
AF:
0.0108
Gnomad4 OTH
AF:
0.0676
Alfa
AF:
0.0439
Hom.:
183
Bravo
AF:
0.106
Asia WGS
AF:
0.0200
AC:
69
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
CADD
Benign
2.8
DANN
Benign
0.66

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs16949816; hg19: chr18-46222367; API