rs8090378

Variant summary

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

The NM_014772.3(CTIF):​c.508-16749T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,288 control chromosomes in the GnomAD database, including 3,664 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 0.15 ( 3664 hom., cov: 33)

Consequence

CTIF
NM_014772.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.75
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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CTIFNM_014772.3 linkuse as main transcriptc.508-16749T>C intron_variant ENST00000256413.8
LOC105372107XR_007066460.1 linkuse as main transcriptn.9556A>G 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.508-16749T>C intron_variant 1 NM_014772.3 A1O43310-1

Frequencies

GnomAD3 genomes
AF:
0.145
AC:
22118
AN:
152170
Hom.:
3643
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.409
Gnomad AMI
AF:
0.00548
Gnomad AMR
AF:
0.0629
Gnomad ASJ
AF:
0.0744
Gnomad EAS
AF:
0.000960
Gnomad SAS
AF:
0.0267
Gnomad FIN
AF:
0.0841
Gnomad MID
AF:
0.0791
Gnomad NFE
AF:
0.0396
Gnomad OTH
AF:
0.101
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.146
AC:
22192
AN:
152288
Hom.:
3664
Cov.:
33
AF XY:
0.143
AC XY:
10627
AN XY:
74474
show subpopulations
Gnomad4 AFR
AF:
0.410
Gnomad4 AMR
AF:
0.0628
Gnomad4 ASJ
AF:
0.0744
Gnomad4 EAS
AF:
0.000963
Gnomad4 SAS
AF:
0.0267
Gnomad4 FIN
AF:
0.0841
Gnomad4 NFE
AF:
0.0396
Gnomad4 OTH
AF:
0.0998
Alfa
AF:
0.107
Hom.:
280
Bravo
AF:
0.157
Asia WGS
AF:
0.0390
AC:
137
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.38
DANN
Benign
0.43

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: rs8090378; hg19: chr18-46221241; API