Genetic Variant RPL7:c.124-13T>A (chr8-73292418-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_000971.4(RPL7):c.124-13T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 1,586,164 control chromosomes in the GnomAD database, including 121,299 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. There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.41 ( 12817 hom., cov: 31)

Exomes 𝑓: 0.38 ( 108482 hom. )

Consequence

RPL7
NM_000971.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.85

Variant links:

Genes affected

RPL7 (HGNC:10363): (ribosomal protein L7) 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 L30P family of ribosomal proteins. It contains an N-terminal basic region-leucine zipper (BZIP)-like domain and the RNP consensus submotif RNP2. In vitro the BZIP-like domain mediates homodimerization and stable binding to DNA and RNA, with a preference for 28S rRNA and mRNA. The protein can inhibit cell-free translation of mRNAs, suggesting that it plays a regulatory role in the translation apparatus. It is located in the cytoplasm. The protein has been shown to be an autoantigen in patients with systemic autoimmune diseases, such as systemic lupus erythematosus. 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]

RPL7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

This position, referring to a specific DNA site, is a probable branch point but is likely benign (scored 1 / 10, using the threshold of <=3). The score ranges from 0 to 10, with values ≤3 considered benign and >5 classified as pathogenic. Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL7	NM_000971.4 link	c.124-13T>A		intron_variant	Intron 2 of 6	ENST00000352983.7	NP_000962.2	P18124
RPL7	NM_001363737.2 link	c.4-13T>A		intron_variant	Intron 2 of 6		NP_001350666.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL7	ENST00000352983.7 link	c.124-13T>A		intron_variant	Intron 2 of 6	1	NM_000971.4	ENSP00000339795.2		P18124

Frequencies

GnomAD3 genomes

AF:

0.407

AC:

61755

AN:

151810

Hom.:

12796

Cov.:

show subpopulations

Gnomad AFR

AF:

0.426

Gnomad AMI

AF:

0.403

Gnomad AMR

AF:

0.451

Gnomad ASJ

AF:

0.347

Gnomad EAS

AF:

0.500

Gnomad SAS

AF:

0.566

Gnomad FIN

AF:

0.465

Gnomad MID

AF:

0.402

Gnomad NFE

AF:

0.362

Gnomad OTH

AF:

0.365

GnomAD3 exomes

AF:

0.428

AC:

99409

AN:

231994

Hom.:

22007

AF XY:

0.430

AC XY:

54397

AN XY:

126632

show subpopulations

Gnomad AFR exome

AF:

0.424

Gnomad AMR exome

AF:

0.507

Gnomad ASJ exome

AF:

0.356

Gnomad EAS exome

AF:

0.511

Gnomad SAS exome

AF:

0.546

Gnomad FIN exome

AF:

0.460

Gnomad NFE exome

AF:

0.366

Gnomad OTH exome

AF:

0.379

GnomAD4 exome

AF:

0.384

AC:

550603

AN:

1434236

Hom.:

108482

Cov.:

AF XY:

0.388

AC XY:

276246

AN XY:

712178

show subpopulations

Gnomad4 AFR exome

AF:

0.423

Gnomad4 AMR exome

AF:

0.499

Gnomad4 ASJ exome

AF:

0.346

Gnomad4 EAS exome

AF:

0.486

Gnomad4 SAS exome

AF:

0.541

Gnomad4 FIN exome

AF:

0.456

Gnomad4 NFE exome

AF:

0.361

Gnomad4 OTH exome

AF:

0.390

GnomAD4 genome

AF:

0.407

AC:

61812

AN:

151928

Hom.:

12817

Cov.:

AF XY:

0.416

AC XY:

30861

AN XY:

74262

show subpopulations

Gnomad4 AFR

AF:

0.426

Gnomad4 AMR

AF:

0.451

Gnomad4 ASJ

AF:

0.347

Gnomad4 EAS

AF:

0.500

Gnomad4 SAS

AF:

0.566

Gnomad4 FIN

AF:

0.465

Gnomad4 NFE

AF:

0.362

Gnomad4 OTH

AF:

0.362

Alfa

AF:

0.286

Hom.:

1115

Bravo

AF:

0.403

Asia WGS

AF:

0.536

AC:

1870

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

0.017

DANN

Benign

0.57

BranchPoint Hunter

1.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over