rs29281

Positions:

chrX-147929961-G-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002024.6(FMR1):c.433G>T(p.Ala145Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00499 in 1,191,575 control chromosomes in the GnomAD database, including 192 homozygotes. There are 1,528 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.025 ( 103 hom., 727 hem., cov: 22)

Exomes 𝑓: 0.0029 ( 89 hom. 801 hem. )

Consequence

FMR1
NM_002024.6 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 4.97

Variant links:

Genes affected

FMR1 (HGNC:3775): (fragile X messenger ribonucleoprotein 1) The protein encoded by this gene binds RNA and is associated with polysomes. The encoded protein may be involved in mRNA trafficking from the nucleus to the cytoplasm. A trinucleotide repeat (CGG) in the 5' UTR is normally found at 6-53 copies, but an expansion to 55-230 repeats is the cause of fragile X syndrome. Expansion of the trinucleotide repeat may also cause one form of premature ovarian failure (POF1). Multiple alternatively spliced transcript variants that encode different protein isoforms and which are located in different cellular locations have been described for this gene. [provided by RefSeq, May 2010]

FMR1 links:

FMR1 (HGNC:):

FMR1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0017594695).

BP6

Variant X-147929961-G-T is Benign according to our data. Variant chrX-147929961-G-T is described in ClinVar as [Benign]. Clinvar id is 129104.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FMR1	NM_002024.6 linkuse as main transcript	c.433G>T	p.Ala145Ser	missense_variant	6/17	ENST00000370475.9	NP_002015.1	Q06787-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FMR1	ENST00000370475.9 linkuse as main transcript	c.433G>T	p.Ala145Ser	missense_variant	6/17	1	NM_002024.6	ENSP00000359506.5		Q06787-1

Frequencies

GnomAD3 genomes

AF:

0.0254

AC:

2820

AN:

110893

Hom.:

103

Cov.:

AF XY:

0.0217

AC XY:

721

AN XY:

33203

show subpopulations

Gnomad AFR

AF:

0.0882

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00931

Gnomad ASJ

AF:

0.000758

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000375

Gnomad FIN

AF:

0.000506

Gnomad MID

AF:

0.0125

Gnomad NFE

AF:

0.000208

Gnomad OTH

AF:

0.0188

GnomAD3 exomes

AF:

0.00772

AC:

1396

AN:

180837

Hom.:

AF XY:

0.00445

AC XY:

293

AN XY:

65783

show subpopulations

Gnomad AFR exome

AF:

0.0911

Gnomad AMR exome

AF:

0.00545

Gnomad ASJ exome

AF:

0.00108

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000268

Gnomad FIN exome

AF:

0.000503

Gnomad NFE exome

AF:

0.000298

Gnomad OTH exome

AF:

0.00404

GnomAD4 exome

AF:

0.00289

AC:

3122

AN:

1080631

Hom.:

Cov.:

AF XY:

0.00230

AC XY:

801

AN XY:

348921

show subpopulations

Gnomad4 AFR exome

AF:

0.0893

Gnomad4 AMR exome

AF:

0.00610

Gnomad4 ASJ exome

AF:

0.00151

Gnomad4 EAS exome

AF:

0.0000332

Gnomad4 SAS exome

AF:

0.000392

Gnomad4 FIN exome

AF:

0.000741

Gnomad4 NFE exome

AF:

0.000243

Gnomad4 OTH exome

AF:

0.00651

GnomAD4 genome

AF:

0.0255

AC:

2826

AN:

110944

Hom.:

103

Cov.:

AF XY:

0.0219

AC XY:

727

AN XY:

33264

show subpopulations

Gnomad4 AFR

AF:

0.0882

Gnomad4 AMR

AF:

0.00930

Gnomad4 ASJ

AF:

0.000758

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000376

Gnomad4 FIN

AF:

0.000506

Gnomad4 NFE

AF:

0.000208

Gnomad4 OTH

AF:

0.0186

Alfa

AF:

0.00526

Hom.:

131

Bravo

AF:

0.0303

TwinsUK

AF:

0.000539

AC:

ALSPAC

AF:

0.000346

AC:

ESP6500AA

AF:

0.0920

AC:

353

ESP6500EA

AF:

0.000446

AC:

ExAC

AF:

0.00850

AC:

1032

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:2

Likely benign, no assertion criteria provided	clinical testing	Genetic Services Laboratory, University of Chicago	-	Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Mar 26, 2018	- -

Inborn genetic diseases

Benign:1

Benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 24, 2014

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Fragile X syndrome

Benign:1

Benign, no assertion criteria provided

clinical testing

Natera, Inc.

Sep 16, 2020

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Fragile X syndrome;C1839780:Fragile X-associated tremor/ataxia syndrome;C4552079:Premature ovarian failure 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Apr 12, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.070

BayesDel_addAF

Benign

-0.77

BayesDel_noAF

Benign

-0.81

CADD

Benign

DANN

Benign

0.15

DEOGEN2

Benign

0.0050

T;.;.;.;.;T;T;.;T;T;T;.

FATHMM_MKL

Benign

0.26

LIST_S2

Benign

0.54

T;T;T;T;T;T;.;T;T;T;T;T

MetaRNN

Benign

0.0018

T;T;T;T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-1.7

.;N;N;N;.;.;.;.;N;.;.;N

PrimateAI

Uncertain

0.70

PROVEAN

Benign

2.4

.;N;N;.;N;.;N;N;N;.;.;N

REVEL

Benign

0.15

Sift

Benign

1.0

.;T;T;.;T;.;T;T;T;.;.;T

Sift4G

Benign

1.0

T;T;T;T;T;T;T;T;T;T;T;T

Polyphen

0.0

.;.;.;B;.;B;B;B;B;.;.;.

Vest4

0.11

MVP

0.62

MPC

0.81

ClinPred

0.0020

GERP RS

4.1

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.32

gMVP

0.31

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