Variant rs2070991 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_012280.4(FTSJ1):c.572-35C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 1,146,737 control chromosomes in the GnomAD database, including 21,056 homozygotes. There are 82,322 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.23 ( 2302 hom., 7789 hem., cov: 23)

Exomes 𝑓: 0.22 ( 18754 hom. 74533 hem. )

Consequence

FTSJ1
NM_012280.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.00200

Variant links:

Genes affected

FTSJ1 (HGNC:13254): (FtsJ RNA 2'-O-methyltransferase 1) This gene encodes a member of the methyltransferase superfamily. The encoded protein localizes to the nucleolus, binds to S-adenosylmethionine, and may be involved in the processing and modification of ribosomal RNA. Mutations in this gene are associated with cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

FTSJ1 links:

FTSJ1 (HGNC:):

FTSJ1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

This place is a probable branch point but likely benign (scored 0 / 10). Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant X-48481597-C-T is Benign according to our data. Variant chrX-48481597-C-T is described in ClinVar as [Benign]. Clinvar id is 1285660.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FTSJ1	NM_012280.4 linkuse as main transcript	c.572-35C>T		intron_variant		ENST00000348411.3	NP_036412.1	Q9UET6-1A0A024QYX5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FTSJ1	ENST00000348411.3 linkuse as main transcript	c.572-35C>T		intron_variant		1	NM_012280.4	ENSP00000326948.2		Q9UET6-1

Frequencies

GnomAD3 genomes

AF:

0.231

AC:

25860

AN:

111801

Hom.:

2304

Cov.:

AF XY:

0.229

AC XY:

7778

AN XY:

34027

show subpopulations

Gnomad AFR

AF:

0.251

Gnomad AMI

AF:

0.187

Gnomad AMR

AF:

0.315

Gnomad ASJ

AF:

0.201

Gnomad EAS

AF:

0.465

Gnomad SAS

AF:

0.347

Gnomad FIN

AF:

0.164

Gnomad MID

AF:

0.148

Gnomad NFE

AF:

0.192

Gnomad OTH

AF:

0.243

GnomAD3 exomes

AF:

0.263

AC:

47020

AN:

179091

Hom.:

4679

AF XY:

0.257

AC XY:

16468

AN XY:

63981

show subpopulations

Gnomad AFR exome

AF:

0.254

Gnomad AMR exome

AF:

0.382

Gnomad ASJ exome

AF:

0.208

Gnomad EAS exome

AF:

0.471

Gnomad SAS exome

AF:

0.351

Gnomad FIN exome

AF:

0.168

Gnomad NFE exome

AF:

0.192

Gnomad OTH exome

AF:

0.241

GnomAD4 exome

AF:

0.224

AC:

232085

AN:

1034885

Hom.:

18754

Cov.:

AF XY:

0.237

AC XY:

74533

AN XY:

314697

show subpopulations

Gnomad4 AFR exome

AF:

0.259

Gnomad4 AMR exome

AF:

0.374

Gnomad4 ASJ exome

AF:

0.211

Gnomad4 EAS exome

AF:

0.445

Gnomad4 SAS exome

AF:

0.353

Gnomad4 FIN exome

AF:

0.177

Gnomad4 NFE exome

AF:

0.201

Gnomad4 OTH exome

AF:

0.239

GnomAD4 genome

AF:

0.231

AC:

25860

AN:

111852

Hom.:

2302

Cov.:

AF XY:

0.228

AC XY:

7789

AN XY:

34088

show subpopulations

Gnomad4 AFR

AF:

0.251

Gnomad4 AMR

AF:

0.314

Gnomad4 ASJ

AF:

0.201

Gnomad4 EAS

AF:

0.465

Gnomad4 SAS

AF:

0.345

Gnomad4 FIN

AF:

0.164

Gnomad4 NFE

AF:

0.192

Gnomad4 OTH

AF:

0.243

Alfa

AF:

0.211

Hom.:

1828

Bravo

AF:

0.250

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	GeneDx	Jun 19, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.1

DANN

Benign

0.73

BranchPoint Hunter

0.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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