Variant X-101391786-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2

The NM_021029.6(RPL36A):c.141C>T(p.Gly47=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00635 in 1,208,700 control chromosomes in the GnomAD database, including 18 homozygotes. There are 2,493 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0042 ( 2 hom., 141 hem., cov: 22)

Exomes 𝑓: 0.0066 ( 16 hom. 2352 hem. )

Consequence

RPL36A
NM_021029.6 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.06

Variant links:

Genes affected

RPL36A (HGNC:10359): (ribosomal protein L36a) Cytoplasmic ribosomes, 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, which shares sequence similarity with yeast ribosomal protein L44, belongs to the L44E (L36AE) family of ribosomal proteins. Although this gene has been referred to as ribosomal protein L44 (RPL44), its official name is ribosomal protein L36a (RPL36A). This gene and the human gene officially named ribosomal protein L36a-like (RPL36AL) encode nearly identical proteins; however, they are distinct genes. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Naturally occurring read-through transcription occurs between this locus and the heterogeneous nuclear ribonucleoprotein H2 (H') gene. [provided by RefSeq, Jan 2011]

RPL36A links:

RPL36A-HNRNPH2 (HGNC:):

RPL36A-HNRNPH2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.41).

BP6

Variant X-101391786-C-T is Benign according to our data. Variant chrX-101391786-C-T is described in ClinVar as [Benign]. Clinvar id is 708163.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-101391786-C-T is described in Lovd as [Likely_benign].

BP7

Synonymous conserved (PhyloP=-1.06 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
RPL36A	NM_021029.6 linkuse as main transcript	c.141C>T	p.Gly47=	synonymous_variant	3/5	ENST00000553110.8
RPL36A-HNRNPH2	NM_001199973.2 linkuse as main transcript	c.141C>T	p.Gly47=	synonymous_variant	3/5
RPL36A-HNRNPH2	NM_001199974.2 linkuse as main transcript	c.141C>T	p.Gly47=	synonymous_variant	3/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPL36A	ENST00000553110.8 linkuse as main transcript	c.141C>T	p.Gly47=	synonymous_variant	3/5	1	NM_021029.6	P1

Frequencies

GnomAD3 genomes

AF:

0.00421

AC:

470

AN:

111760

Hom.:

Cov.:

AF XY:

0.00416

AC XY:

141

AN XY:

33916

show subpopulations

Gnomad AFR

AF:

0.000879

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00516

Gnomad ASJ

AF:

0.00188

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00111

Gnomad FIN

AF:

0.00283

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00675

Gnomad OTH

AF:

0.00332

GnomAD3 exomes

AF:

0.00407

AC:

738

AN:

181291

Hom.:

AF XY:

0.00393

AC XY:

259

AN XY:

65843

show subpopulations

Gnomad AFR exome

AF:

0.000228

Gnomad AMR exome

AF:

0.00115

Gnomad ASJ exome

AF:

0.00136

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00179

Gnomad FIN exome

AF:

0.00313

Gnomad NFE exome

AF:

0.00733

Gnomad OTH exome

AF:

0.00334

GnomAD4 exome

AF:

0.00657

AC:

7204

AN:

1096883

Hom.:

Cov.:

AF XY:

0.00649

AC XY:

2352

AN XY:

362297

show subpopulations

Gnomad4 AFR exome

AF:

0.000646

Gnomad4 AMR exome

AF:

0.00129

Gnomad4 ASJ exome

AF:

0.00192

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00201

Gnomad4 FIN exome

AF:

0.00385

Gnomad4 NFE exome

AF:

0.00783

Gnomad4 OTH exome

AF:

0.00528

GnomAD4 genome

AF:

0.00420

AC:

470

AN:

111817

Hom.:

Cov.:

AF XY:

0.00415

AC XY:

141

AN XY:

33983

show subpopulations

Gnomad4 AFR

AF:

0.000877

Gnomad4 AMR

AF:

0.00515

Gnomad4 ASJ

AF:

0.00188

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00111

Gnomad4 FIN

AF:

0.00283

Gnomad4 NFE

AF:

0.00675

Gnomad4 OTH

AF:

0.00327

Alfa

AF:

0.00486

Hom.:

Bravo

AF:

0.00430

EpiCase

AF:

0.00551

EpiControl

AF:

0.00854

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Mar 29, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.41

CADD

Benign

DANN

Benign

0.93

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over