rs5905692

Positions:

• chrX-48483367-T-C
• chrX-48483367-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012280.4(FTSJ1):​c.*9+340T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 240,432 control chromosomes in the GnomAD database, including 13,224 homozygotes. There are 25,233 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.38 (8242 hom., 12168 hem., cov: 22)
  • Exomes 𝑓: 0.33 (4982 hom. 13065 hem.)
• Consequence: FTSJ1 NM_012280.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.753 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FTSJ1	NM_012280.4	c.*9+340T>C		intron_variant		ENST00000348411.3	NP_036412.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FTSJ1	ENST00000348411.3	c.*9+340T>C		intron_variant		1	NM_012280.4	ENSP00000326948.2

Frequencies

GnomAD3 genomes AF: 0.380 AC: 42137 AN: 110795 Hom.: 8243 Cov.: 22 AF XY: 0.367 AC XY: 12140 AN XY: 33055

Gnomad AFR AF: 0.762

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.202

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.366

GnomAD4 exome AF: 0.332 AC: 42982 AN: 129595 Hom.: 4982 Cov.: 0 AF XY: 0.481 AC XY: 13065 AN XY: 27157

Gnomad4 AFR exome AF: 0.801

Gnomad4 AMR exome AF: 0.445

Gnomad4 ASJ exome AF: 0.285

Gnomad4 EAS exome AF: 0.512

Gnomad4 SAS exome AF: 0.542

Gnomad4 FIN exome AF: 0.254

Gnomad4 NFE exome AF: 0.251

Gnomad4 OTH exome AF: 0.333

GnomAD4 genome AF: 0.380 AC: 42156 AN: 110837 Hom.: 8242 Cov.: 22 AF XY: 0.368 AC XY: 12168 AN XY: 33107

Gnomad4 AFR AF: 0.761

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.364

Alfa AF: 0.226 Hom.: 16213

Bravo AF: 0.419

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.28
DANN	Benign	0.69

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

Other links and lift over

dbSNP: rs5905692; hg19: chrX-48341755;