rs745398301

Variant names:

• chr2-27137452-C-G
• rs745398301
• NM_178553.4:c.878G>C

Your query was ambiguous. Multiple possible variants found:

• chr2-27137452-C-G
• chr2-27137452-C-T

Variant summary

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

The NM_178553.4(PRR30):​c.878G>C​(p.Arg293Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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. R293Q) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PRR30 NM_178553.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.854
• Publications: 1 publications found

Genes affected

PRR30 (HGNC:28677): (proline rich 30)

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178553.4. 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
	PRR30	NM_178553.4	MANE Select	c.878G>C	p.Arg293Pro	missense	Exon 3 of 3	NP_848648.2	Q53SZ7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRR30	ENST00000335524.7	TSL:1 MANE Select	c.878G>C	p.Arg293Pro	missense	Exon 3 of 3	ENSP00000335017.3	Q53SZ7
	PRR30	ENST00000432962.2	TSL:3	c.384G>C	p.Pro128Pro	synonymous	Exon 4 of 4	ENSP00000393468.2	C9JVA3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.63
BayesDel_addAF	Benign	0.0026	T
BayesDel_noAF	Benign	-0.23
CADD	Benign	20
DANN	Uncertain	1.0
DEOGEN2	Benign	0.045	T
Eigen	Benign	0.15
Eigen_PC	Benign	0.063
FATHMM_MKL	Benign	0.46	N
LIST_S2	Benign	0.54	T
M_CAP	Benign	0.011	T
MetaRNN	Uncertain	0.73	D
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.4	L
PhyloP100		0.85
PROVEAN	Pathogenic	-5.3	D
REVEL	Benign	0.15
Sift	Uncertain	0.0040	D
Sift4G	Benign	0.26	T
Polyphen		1.0	D
Vest4		0.73
MutPred		0.48		Loss of MoRF binding (P = 0.0292)
MVP		0.29
MPC		0.82
ClinPred		0.99	D
GERP RS		2.8
Varity_R		0.62
gMVP		0.93
Mutation Taster		=91/9	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: rs745398301; hg19: chr2-27360320;