5-120481255-C-A

Variant names:

• chr5-120481255-C-A
• ENST00000379551.2:c.52C>A

Variant summary

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

The NM_016644.3(PRR16):​c.52C>A​(p.Leu18Ile) 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. 14/19 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: PRR16 NM_016644.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -0.377
• Publications: 0 publications found

Genes affected

PRR16 (HGNC:29654): (proline rich 16) Involved in positive regulation of cell size and positive regulation of translation. [provided by Alliance of Genome Resources, Apr 2022]

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=0.10516569).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016644.3. 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
	PRR16	NM_001300783.2	MANE Select	c.159+16610C>A		intron	N/A	NP_001287712.1	Q569H4-1
	PRR16	NM_016644.3		c.52C>A	p.Leu18Ile	missense	Exon 2 of 3	NP_057728.1	Q569H4-3
	PRR16	NM_001308087.2		c.-52+15544C>A		intron	N/A	NP_001295016.1	Q569H4-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRR16	ENST00000379551.2	TSL:1	c.52C>A	p.Leu18Ile	missense	Exon 2 of 3	ENSP00000368869.2	Q569H4-3
	PRR16	ENST00000407149.7	TSL:1 MANE Select	c.159+16610C>A		intron	N/A	ENSP00000385118.2	Q569H4-1
	PRR16	ENST00000509923.1	TSL:3	c.-52+15544C>A		intron	N/A	ENSP00000421256.1	D6RGF0

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 4

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	0.096
BayesDel_addAF	Benign	-0.27	T
BayesDel_noAF	Benign	-0.62
CADD	Benign	2.1
DANN	Benign	0.96
Eigen	Benign	-0.75
Eigen_PC	Benign	-0.99
FATHMM_MKL	Benign	0.0024	N
LIST_S2	Benign	0.22	T
M_CAP	Benign	0.0020	T
MetaRNN	Benign	0.11	T
MetaSVM	Benign	-0.99	T
PhyloP100		-0.38
PrimateAI	Uncertain	0.55	T
PROVEAN	Benign	-0.38	N
REVEL	Benign	0.041
Sift	Pathogenic	0.0	D
Sift4G	Benign	0.74	T
Polyphen		0.59	P
Vest4		0.16
MutPred		0.25		Gain of sheet (P = 0.0149)
MVP		0.093
MPC		0.041
ClinPred		0.66	D
GERP RS		0.16
Mutation Taster		=100/0	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: chr5-119816950;