X-101391786-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP6_Very_StrongBP7BS2

The NM_021029.6(RPL36A):c.141C>T(p.Gly47Gly) 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. 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

Publications

2 publications found

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:48349): (RPL36A-HNRNPH2 readthrough) This locus represents naturally occurring read-through transcription between the neighboring ribosomal protein L36a and heterogeneous nuclear ribonucleoprotein H2 (H') genes on chromosome X. The read-through transcript produces a protein with similarity to the protein encoded by the upstream locus, ribosomal protein L36a. Alternatively spliced transcript variants have been identified. [provided by RefSeq, Jan 2011]

RPL36A-HNRNPH2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

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.

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 rank	MANE	Protein	UniProt
RPL36A	NM_021029.6 link	c.141C>T	p.Gly47Gly	synonymous_variant	Exon 3 of 5	ENST00000553110.8	NP_066357.3	P83881J3KQN4
RPL36A-HNRNPH2	NM_001199973.2 link	c.141C>T	p.Gly47Gly	synonymous_variant	Exon 3 of 5		NP_001186902.2
RPL36A-HNRNPH2	NM_001199974.2 link	c.141C>T	p.Gly47Gly	synonymous_variant	Exon 3 of 4		NP_001186903.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL36A	ENST00000553110.8 link	c.141C>T	p.Gly47Gly	synonymous_variant	Exon 3 of 5	1	NM_021029.6	ENSP00000446503.2		P83881
RPL36A-HNRNPH2	ENST00000409170.3 link	c.141C>T	p.Gly47Gly	synonymous_variant	Exon 3 of 5	4		ENSP00000386655.4		H7BZ11

Frequencies

GnomAD3 genomes

AF:

0.00421

AC:

470

AN:

111760

Hom.:

Cov.:

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

GnomAD2 exomes

AF:

0.00407

AC:

738

AN:

181291

AF XY:

0.00393

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 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

African (AFR)

AF:

0.000646

AC:

AN:

26324

American (AMR)

AF:

0.00129

AC:

AN:

34870

Ashkenazi Jewish (ASJ)

AF:

0.00192

AC:

AN:

19309

East Asian (EAS)

AF:

0.00

AC:

AN:

30199

South Asian (SAS)

AF:

0.00201

AC:

108

AN:

53682

European-Finnish (FIN)

AF:

0.00385

AC:

156

AN:

40519

Middle Eastern (MID)

AF:

0.00170

AC:

AN:

4125

European-Non Finnish (NFE)

AF:

0.00783

AC:

6591

AN:

841800

Other (OTH)

AF:

0.00528

AC:

243

AN:

46055

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

308

617

925

1234

1542

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.00420

AC:

470

AN:

111817

Hom.:

Cov.:

AF XY:

0.00415

AC XY:

141

AN XY:

33983

show subpopulations

African (AFR)

AF:

0.000877

AC:

AN:

30795

American (AMR)

AF:

0.00515

AC:

AN:

10485

Ashkenazi Jewish (ASJ)

AF:

0.00188

AC:

AN:

2653

East Asian (EAS)

AF:

0.00

AC:

AN:

3553

South Asian (SAS)

AF:

0.00111

AC:

AN:

2693

European-Finnish (FIN)

AF:

0.00283

AC:

AN:

6017

Middle Eastern (MID)

AF:

0.00

AC:

AN:

219

European-Non Finnish (NFE)

AF:

0.00675

AC:

359

AN:

53190

Other (OTH)

AF:

0.00327

AC:

AN:

1528

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

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

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Mar 29, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.41

CADD

Benign

(source)

DANN

Benign

0.93

PhyloP100

-1.1

Mutation Taster

=298/2

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

X-101391786-C-T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over