Variant chr3-40462029-A-ACTGCTGCTGCTGCTG details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001034996.3(RPL14):c.463_477dup(p.Ala155_Ala159dup) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.27 ( 6524 hom., cov: 0)

Exomes 𝑓: 0.29 ( 36787 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]

RPL14 links:

Genome browser will be placed here

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-ACTGCTGCTGCTGCTG is Benign according to our data. Variant chr3-40462029-A-ACTGCTGCTGCTGCTG is described in ClinVar as [Benign]. Clinvar id is 770139.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RPL14	NM_001034996.3 linkuse as main transcript	c.463_477dup	p.Ala155_Ala159dup	inframe_insertion	6/6	ENST00000396203.7	NP_001030168.1
RPL14	NM_003973.5 linkuse as main transcript	c.463_477dup	p.Ala155_Ala159dup	inframe_insertion	6/6		NP_003964.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RPL14	ENST00000396203.7 linkuse as main transcript	c.463_477dup	p.Ala155_Ala159dup	inframe_insertion	6/6	1	NM_001034996.3	ENSP00000379506	P1

Frequencies

GnomAD3 genomes

AF:

0.272

AC:

40291

AN:

148174

Hom.:

6526

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0903

Gnomad AMI

AF:

0.446

Gnomad AMR

AF:

0.256

Gnomad ASJ

AF:

0.331

Gnomad EAS

AF:

0.182

Gnomad SAS

AF:

0.240

Gnomad FIN

AF:

0.368

Gnomad MID

AF:

0.374

Gnomad NFE

AF:

0.369

Gnomad OTH

AF:

0.280

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.292

AC:

395686

AN:

1355340

Hom.:

36787

Cov.:

AF XY:

0.290

AC XY:

195548

AN XY:

673824

show subpopulations

Gnomad4 AFR exome

AF:

0.0749

Gnomad4 AMR exome

AF:

0.214

Gnomad4 ASJ exome

AF:

0.281

Gnomad4 EAS exome

AF:

0.194

Gnomad4 SAS exome

AF:

0.215

Gnomad4 FIN exome

AF:

0.308

Gnomad4 NFE exome

AF:

0.312

Gnomad4 OTH exome

AF:

0.275

GnomAD4 genome

AF:

0.272

AC:

40283

AN:

148282

Hom.:

6524

Cov.:

AF XY:

0.272

AC XY:

19644

AN XY:

72224

show subpopulations

Gnomad4 AFR

AF:

0.0901

Gnomad4 AMR

AF:

0.255

Gnomad4 ASJ

AF:

0.331

Gnomad4 EAS

AF:

0.183

Gnomad4 SAS

AF:

0.240

Gnomad4 FIN

AF:

0.368

Gnomad4 NFE

AF:

0.369

Gnomad4 OTH

AF:

0.279

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 submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over