rs9610529

Variant summary

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

The NM_003753.4(EIF3D):​c.-11+1251A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 152,060 control chromosomes in the GnomAD database, including 9,150 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 0.31 ( 9150 hom., cov: 32)

Consequence

EIF3D
NM_003753.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.105
Variant links:
Genes affected
EIF3D (HGNC:3278): (eukaryotic translation initiation factor 3 subunit D) Eukaryotic translation initiation factor-3 (eIF3), the largest of the eIFs, is a multiprotein complex composed of at least ten nonidentical subunits. The complex binds to the 40S ribosome and helps maintain the 40S and 60S ribosomal subunits in a dissociated state. It is also thought to play a role in the formation of the 40S initiation complex by interacting with the ternary complex of eIF2/GTP/methionyl-tRNA, and by promoting mRNA binding. The protein encoded by this gene is the major RNA binding subunit of the eIF3 complex. [provided by RefSeq, Jul 2008]

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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=-0.87).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
EIF3DNM_003753.4 linkc.-11+1251A>G intron_variant Intron 1 of 14 ENST00000216190.13 NP_003744.1 O15371-1
EIF3DXM_047441560.1 linkc.-11+1251A>G intron_variant Intron 1 of 9 XP_047297516.1
EIF3DNR_156418.2 linkn.91+1251A>G intron_variant Intron 1 of 14

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
EIF3DENST00000216190.13 linkc.-11+1251A>G intron_variant Intron 1 of 14 1 NM_003753.4 ENSP00000216190.8 O15371-1

Frequencies

GnomAD3 genomes
AF:
0.306
AC:
46540
AN:
151942
Hom.:
9122
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.562
Gnomad AMI
AF:
0.148
Gnomad AMR
AF:
0.263
Gnomad ASJ
AF:
0.194
Gnomad EAS
AF:
0.00732
Gnomad SAS
AF:
0.118
Gnomad FIN
AF:
0.186
Gnomad MID
AF:
0.123
Gnomad NFE
AF:
0.226
Gnomad OTH
AF:
0.248
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.307
AC:
46620
AN:
152060
Hom.:
9150
Cov.:
32
AF XY:
0.298
AC XY:
22186
AN XY:
74336
show subpopulations
Gnomad4 AFR
AF:
0.562
Gnomad4 AMR
AF:
0.263
Gnomad4 ASJ
AF:
0.194
Gnomad4 EAS
AF:
0.00734
Gnomad4 SAS
AF:
0.118
Gnomad4 FIN
AF:
0.186
Gnomad4 NFE
AF:
0.226
Gnomad4 OTH
AF:
0.245
Alfa
AF:
0.191
Hom.:
607
Bravo
AF:
0.326
Asia WGS
AF:
0.0980
AC:
343
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
5.4
DANN
Benign
0.59

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: rs9610529; hg19: chr22-36923872; API