rs1055025

Variant names:

• chrX-129929497-A-G
• rs1055025
• NM_006649.4:c.2205A>G

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_006649.4(UTP14A):​c.2205A>G​(p.Glu735Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 23)
• Consequence: UTP14A NM_006649.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.62
• Publications: 1 publications found

Genes affected

UTP14A (HGNC:10665): (UTP14A small subunit processome component) This gene encodes a member of the uridine triphosphate 14 family. As an essential component of a large ribonucleoprotein complex bound to the U3 small nucleolar RNA, the encoded protein is involved in ribosome biogenesis and 18S rRNA synthesis. An autosomal retrotransposed copy of this X-linked gene exists on chromosome 13. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Oct 2009]

ENSG00000235189 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BP7: Synonymous conserved (PhyloP=1.62 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006649.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UTP14A	NM_006649.4	MANE Select	c.2205A>G	p.Glu735Glu	synonymous	Exon 15 of 15	NP_006640.2
	UTP14A	NM_001166221.2		c.2049A>G	p.Glu683Glu	synonymous	Exon 14 of 14	NP_001159693.1	Q9BVJ6-3
	LOC105373335	NR_188631.1		n.218+261T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UTP14A	ENST00000394422.8	TSL:1 MANE Select	c.2205A>G	p.Glu735Glu	synonymous	Exon 15 of 15	ENSP00000377944.3	Q9BVJ6-1
	UTP14A	ENST00000956766.1		c.2229A>G	p.Glu743Glu	synonymous	Exon 15 of 15	ENSP00000626825.1
	UTP14A	ENST00000869131.1		c.2226A>G	p.Glu742Glu	synonymous	Exon 15 of 15	ENSP00000539190.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	6.1
DANN	Benign	0.59
PhyloP100		1.6

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

Other links and lift over

dbSNP: rs1055025; hg19: chrX-129063473;