22-31713654-C-A

Variant names:

• chr22-31713654-C-A
• rs3804090
• NM_173566.3:c.4185G>T

Variant summary

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

The NM_173566.3(PRR14L):​c.4185G>T​(p.Leu1395Phe) 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. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PRR14L NM_173566.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 5 publications found

Genes affected

PRR14L (HGNC:28738): (proline rich 14 like)

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=0.08496526).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173566.3. 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
	PRR14L	NM_173566.3	MANE Select	c.4185G>T	p.Leu1395Phe	missense	Exon 4 of 9	NP_775837.2	Q5THK1-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRR14L	ENST00000327423.11	TSL:5 MANE Select	c.4185G>T	p.Leu1395Phe	missense	Exon 4 of 9	ENSP00000331845.6	Q5THK1-1
	PRR14L	ENST00000923610.1		c.4185G>T	p.Leu1395Phe	missense	Exon 4 of 9	ENSP00000593669.1
	PRR14L	ENST00000923611.1		c.4185G>T	p.Leu1395Phe	missense	Exon 4 of 9	ENSP00000593670.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

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	Benign	0.12
BayesDel_addAF	Benign	-0.29	T
BayesDel_noAF	Benign	-0.65
CADD	Benign	11
DANN	Uncertain	0.99
DEOGEN2	Benign	0.0059	T
Eigen	Benign	-0.96
Eigen_PC	Benign	-1.0
FATHMM_MKL	Benign	0.12	N
LIST_S2	Benign	0.44	T
M_CAP	Benign	0.038	D
MetaRNN	Benign	0.085	T
MetaSVM	Benign	-0.95	T
MutationAssessor	Benign	1.8	L
PhyloP100		0.21
PrimateAI	Benign	0.23	T
PROVEAN	Benign	-1.7	N
REVEL	Benign	0.029
Sift	Uncertain	0.0050	D
Sift4G	Uncertain	0.022	D
Polyphen		0.082	B
Vest4		0.046
MutPred		0.073		Loss of disorder (P = 0.1357)
MVP		0.068
MPC		0.073
ClinPred		0.079	T
GERP RS		1.4
Varity_R		0.073
gMVP		0.042
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

dbSNP: rs3804090; hg19: chr22-32109640;