chr22-31458860-T-C

Variant summary

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

The NM_019843.4(EIF4ENIF1):​c.788-210A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.36 in 150,930 control chromosomes in the GnomAD database, including 11,162 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 0.36 ( 11162 hom., cov: 29)

Consequence

EIF4ENIF1
NM_019843.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.312
Variant links:
Genes affected
EIF4ENIF1 (HGNC:16687): (eukaryotic translation initiation factor 4E nuclear import factor 1) The protein encoded by this gene is a nucleocytoplasmic shuttle protein for the translation initiation factor eIF4E. This shuttle protein interacts with the importin alpha-beta complex to mediate nuclear import of eIF4E. It is predominantly cytoplasmic; its own nuclear import is regulated by a nuclear localization signal and nuclear export signals. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2009]
DRG1 (HGNC:3029): (developmentally regulated GTP binding protein 1) Enables several functions, including GTPase activity; identical protein binding activity; and potassium ion binding activity. Involved in positive regulation of microtubule polymerization and regulation of mitotic spindle assembly. Located in cytosol and nuclear body. Part of polysome. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
EIF4ENIF1NM_019843.4 linkuse as main transcriptc.788-210A>G intron_variant ENST00000330125.10 NP_062817.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
EIF4ENIF1ENST00000330125.10 linkuse as main transcriptc.788-210A>G intron_variant 1 NM_019843.4 ENSP00000328103 P1Q9NRA8-1
ENST00000655902.1 linkuse as main transcriptn.1543+4437T>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.360
AC:
54227
AN:
150832
Hom.:
11152
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.214
Gnomad AMI
AF:
0.349
Gnomad AMR
AF:
0.418
Gnomad ASJ
AF:
0.267
Gnomad EAS
AF:
0.869
Gnomad SAS
AF:
0.486
Gnomad FIN
AF:
0.412
Gnomad MID
AF:
0.264
Gnomad NFE
AF:
0.385
Gnomad OTH
AF:
0.334
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.360
AC:
54273
AN:
150930
Hom.:
11162
Cov.:
29
AF XY:
0.366
AC XY:
26946
AN XY:
73566
show subpopulations
Gnomad4 AFR
AF:
0.215
Gnomad4 AMR
AF:
0.418
Gnomad4 ASJ
AF:
0.267
Gnomad4 EAS
AF:
0.870
Gnomad4 SAS
AF:
0.487
Gnomad4 FIN
AF:
0.412
Gnomad4 NFE
AF:
0.385
Gnomad4 OTH
AF:
0.336
Alfa
AF:
0.375
Hom.:
2901
Bravo
AF:
0.354
Asia WGS
AF:
0.641
AC:
2226
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.3
DANN
Benign
0.54

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: rs5753625; hg19: chr22-31854846; API