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GeneBe

3-40462029-A-ACTGCTGCTGCTGCTGCTG

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP3BP6_ModerateBA1

The NM_001034996.3(RPL14):c.460_477dup(p.Ala154_Ala159dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0518 in 148,386 control chromosomes in the GnomAD database, including 240 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.052 ( 240 hom., cov: 0)
Exomes 𝑓: 0.056 ( 2527 hom. )
Failed GnomAD Quality Control

Consequence

RPL14
NM_001034996.3 inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00
Variant links:
Genes affected
RPL14 (HGNC:10305): (ribosomal protein L14) Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L14E family of ribosomal proteins. It contains a basic region-leucine zipper (bZIP)-like domain. The protein is located in the cytoplasm. This gene contains a trinucleotide (GCT) repeat tract whose length is highly polymorphic; these triplet repeats result in a stretch of alanine residues in the encoded protein. Transcript variants utilizing alternative polyA signals and alternative 5'-terminal exons exist but all encode the same protein. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP3
Nonframeshift variant in repetitive region in NM_001034996.3
BP6
Variant 3-40462029-A-ACTGCTGCTGCTGCTGCTG is Benign according to our data. Variant chr3-40462029-A-ACTGCTGCTGCTGCTGCTG is described in ClinVar as [Benign]. Clinvar id is 770140.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0658 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPL14NM_001034996.3 linkuse as main transcriptc.460_477dup p.Ala154_Ala159dup inframe_insertion 6/6 ENST00000396203.7
RPL14NM_003973.5 linkuse as main transcriptc.460_477dup p.Ala154_Ala159dup inframe_insertion 6/6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPL14ENST00000396203.7 linkuse as main transcriptc.460_477dup p.Ala154_Ala159dup inframe_insertion 6/61 NM_001034996.3 P1

Frequencies

GnomAD3 genomes
AF:
0.0519
AC:
7690
AN:
148278
Hom.:
241
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0326
Gnomad AMI
AF:
0.00991
Gnomad AMR
AF:
0.0448
Gnomad ASJ
AF:
0.0510
Gnomad EAS
AF:
0.0267
Gnomad SAS
AF:
0.0280
Gnomad FIN
AF:
0.0625
Gnomad MID
AF:
0.0226
Gnomad NFE
AF:
0.0674
Gnomad OTH
AF:
0.0472
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0563
AC:
78809
AN:
1398724
Hom.:
2527
Cov.:
80
AF XY:
0.0561
AC XY:
38942
AN XY:
694454
show subpopulations
Gnomad4 AFR exome
AF:
0.0276
Gnomad4 AMR exome
AF:
0.0410
Gnomad4 ASJ exome
AF:
0.0565
Gnomad4 EAS exome
AF:
0.0219
Gnomad4 SAS exome
AF:
0.0248
Gnomad4 FIN exome
AF:
0.0644
Gnomad4 NFE exome
AF:
0.0615
Gnomad4 OTH exome
AF:
0.0506
GnomAD4 genome
AF:
0.0518
AC:
7685
AN:
148386
Hom.:
240
Cov.:
0
AF XY:
0.0498
AC XY:
3600
AN XY:
72280
show subpopulations
Gnomad4 AFR
AF:
0.0325
Gnomad4 AMR
AF:
0.0447
Gnomad4 ASJ
AF:
0.0510
Gnomad4 EAS
AF:
0.0262
Gnomad4 SAS
AF:
0.0278
Gnomad4 FIN
AF:
0.0625
Gnomad4 NFE
AF:
0.0674
Gnomad4 OTH
AF:
0.0482

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeDec 31, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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: rs57354599; hg19: chr3-40503520; API