chrX-53428058-C-T

Variant names:

• chrX-53428058-C-T
• NM_001031745.5:c.173C>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001031745.5(RIBC1):​c.173C>T​(p.Ala58Val) variant causes a missense 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. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 23)
• Consequence: RIBC1 NM_001031745.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.816
• Publications: 0 publications found

Genes affected

RIBC1 (HGNC:26537): (RIB43A domain with coiled-coils 1)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.08843264).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001031745.5. 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
	RIBC1	NM_001031745.5	MANE Select	c.173C>T	p.Ala58Val	missense	Exon 4 of 8	NP_001026915.1	Q8N443-1
	RIBC1	NM_001267053.4		c.173C>T	p.Ala58Val	missense	Exon 4 of 6	NP_001253982.1	Q8N443-3
	RIBC1	NM_144968.4		c.173C>T	p.Ala58Val	missense	Exon 4 of 5	NP_659405.1	Q8N443-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RIBC1	ENST00000375327.6	TSL:1 MANE Select	c.173C>T	p.Ala58Val	missense	Exon 4 of 8	ENSP00000364476.3	Q8N443-1
	RIBC1	ENST00000868183.1		c.173C>T	p.Ala58Val	missense	Exon 4 of 8	ENSP00000538242.1
	RIBC1	ENST00000929472.1		c.173C>T	p.Ala58Val	missense	Exon 5 of 9	ENSP00000599531.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 23

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.43	T
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.32
DANN	Benign	0.95
DEOGEN2	Benign	0.014	T
FATHMM_MKL	Benign	0.022	N
LIST_S2	Benign	0.70	T
M_CAP	Benign	0.0053	T
MetaRNN	Benign	0.088	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.81	L
PhyloP100		-0.82
PrimateAI	Benign	0.24	T
PROVEAN	Benign	-0.60	N
REVEL	Benign	0.021
Sift	Benign	0.30	T
Sift4G	Benign	1.0	T
Polyphen		0.021	B
Vest4		0.052
MutPred		0.45		Gain of methylation at K62 (P = 0.0882)
MVP		0.10
MPC		0.23
ClinPred		0.050	T
GERP RS		-3.7
Varity_R		0.053
gMVP		0.15
Mutation Taster		=95/5	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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

hg19: chrX-53455006;