rs147628815

Variant names:

• chr5-126603613-C-G
• rs147628815
• NM_032177.4:c.140C>G

Your query was ambiguous. Multiple possible variants found:

• chr5-126603613-C-G
• chr5-126603613-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_032177.4(PHAX):​c.140C>G​(p.Thr47Arg) 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. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T47M) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PHAX NM_032177.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 0 publications found

Genes affected

PHAX (HGNC:10241): (phosphorylated adaptor for RNA export) Enables mRNA cap binding complex binding activity. Involved in RNA stabilization. Located in centrosome and nucleoplasm. Part of ribonucleoprotein complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.05904469).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032177.4. 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
	PHAX	NM_032177.4	MANE Select	c.140C>G	p.Thr47Arg	missense	Exon 2 of 5	NP_115553.2	Q9H814

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHAX	ENST00000297540.5	TSL:1 MANE Select	c.140C>G	p.Thr47Arg	missense	Exon 2 of 5	ENSP00000297540.4	Q9H814
	PHAX	ENST00000852111.1		c.140C>G	p.Thr47Arg	missense	Exon 2 of 4	ENSP00000522170.1
	PHAX	ENST00000505674.5	TSL:2	n.53C>G		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.10
BayesDel_addAF	Benign	-0.29	T
BayesDel_noAF	Benign	-0.66
CADD	Benign	4.1
DANN	Benign	0.94
DEOGEN2	Benign	0.0090	T
Eigen	Benign	-0.92
Eigen_PC	Benign	-0.87
FATHMM_MKL	Benign	0.056	N
LIST_S2	Benign	0.60	T
M_CAP	Benign	0.0057	T
MetaRNN	Benign	0.059	T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	0.49	N
PhyloP100		1.1
PrimateAI	Benign	0.31	T
PROVEAN	Benign	-0.47	N
REVEL	Benign	0.040
Sift	Benign	0.14	T
Sift4G	Benign	0.18	T
Polyphen		0.0030	B
Vest4		0.14
MutPred		0.19		Gain of MoRF binding (P = 0.0309)
MVP		0.15
MPC		0.10
ClinPred		0.083	T
GERP RS		3.5
Varity_R		0.034
gMVP		0.11
Mutation Taster		=89/11	polymorphism

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: rs147628815; hg19: chr5-125939305;