Genetic Variant FMR1:c.-108_-100delCGGCGGCGG (chrX-147912049-CGCGGCGGCG-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_002024.6(FMR1):c.-108_-100delCGGCGGCGG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000819 in 41,497 control chromosomes in the GnomAD database, including 1 homozygotes. There are 15 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00051 ( 0 hom., 4 hem., cov: 2)

Exomes 𝑓: 0.0025 ( 1 hom. 11 hem. )

Consequence

FMR1
NM_002024.6 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.53

Publications

0 publications found

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-AS1 (HGNC:39081): (FMR1 antisense RNA 1)

FMR1-AS1 links:

ENSG00000274086 (HGNC:):

ENSG00000274086 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6

Variant X-147912049-CGCGGCGGCG-C is Benign according to our data. Variant chrX-147912049-CGCGGCGGCG-C is described in ClinVar as Benign. ClinVar VariationId is 1166634.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.000512 (18/35174) while in subpopulation AMR AF = 0.000725 (2/2760). AF 95% confidence interval is 0.00032. There are 0 homozygotes in GnomAd4. There are 4 alleles in the male GnomAd4 subpopulation. Median coverage is 2. This position passed quality control check.

BS2

High Hemizygotes in GnomAd4 at 4 XL gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002024.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FMR1	NM_002024.6	MANE Select	c.-108_-100delCGGCGGCGG	5_prime_UTR	Exon 1 of 17	NP_002015.1
FMR1	NM_001185076.2		c.-108_-100delCGGCGGCGG	5_prime_UTR	Exon 1 of 16	NP_001172005.1
FMR1	NM_001185082.2		c.-108_-100delCGGCGGCGG	5_prime_UTR	Exon 1 of 16	NP_001172011.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FMR1	ENST00000370475.9	TSL:1 MANE Select	c.-108_-100delCGGCGGCGG	5_prime_UTR	Exon 1 of 17	ENSP00000359506.5
FMR1	ENST00000218200.12	TSL:1	c.-108_-100delCGGCGGCGG	5_prime_UTR	Exon 1 of 16	ENSP00000218200.8
FMR1	ENST00000439526.6	TSL:1	c.-108_-100delCGGCGGCGG	5_prime_UTR	Exon 1 of 16	ENSP00000395923.2

Frequencies

GnomAD3 genomes

AF:

0.000512

AC:

AN:

35174

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000513

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000725

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000570

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00253

AC:

AN:

6323

Hom.:

AF XY:

0.00322

AC XY:

AN XY:

3413

show subpopulations

African (AFR)

AF:

0.0303

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.0103

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00236

AC:

AN:

5930

Other (OTH)

AF:

0.00

AC:

AN:

173

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.608

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000512

AC:

AN:

35174

Hom.:

Cov.:

AF XY:

0.000690

AC XY:

AN XY:

5800

show subpopulations

African (AFR)

AF:

0.000513

AC:

AN:

9740

American (AMR)

AF:

0.000725

AC:

AN:

2760

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

831

East Asian (EAS)

AF:

0.00

AC:

AN:

569

South Asian (SAS)

AF:

0.00

AC:

AN:

426

European-Finnish (FIN)

AF:

0.00

AC:

AN:

836

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.000570

AC:

AN:

19299

Other (OTH)

AF:

0.00

AC:

AN:

465

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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X-147912049-CGCGGCGGCGGCGGCGGCGGCG-CGCGGCGGCGGCG

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over