NM_178553.4:c.799A>G

Variant names:

• chr2-27137531-T-C
• NM_178553.4:c.799A>G

Variant summary

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

The NM_178553.4(PRR30):​c.799A>G​(p.Arg267Gly) 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. 13/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: PRR30 NM_178553.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.25
• Publications: 0 publications found

Genes affected

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

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=0.21567279).

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.799A>G	p.Arg267Gly	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.799A>G	p.Arg267Gly	missense	Exon 3 of 3	ENSP00000335017.3	Q53SZ7
	PRR30	ENST00000432962.2	TSL:3	c.305A>G	p.Gln102Arg	missense	Exon 4 of 4	ENSP00000393468.2	C9JVA3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

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	0.19
BayesDel_addAF	Benign	-0.24	T
BayesDel_noAF	Benign	-0.53
CADD	Benign	21
DANN	Benign	0.97
Eigen	Benign	-0.30
Eigen_PC	Benign	-0.18
FATHMM_MKL	Benign	0.73	D
M_CAP	Benign	0.011	T
MetaRNN	Benign	0.22	T
MetaSVM	Benign	-1.0	T
PhyloP100		2.2
PROVEAN	Uncertain	-4.0	D
REVEL	Benign	0.11
MutPred		0.083		Gain of methylation at Q102 (P = 0.029)
MVP		0.27
ClinPred		0.89	D
GERP RS		4.7
Varity_R		0.30
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

hg19: chr2-27360399;