chr22-31713656-A-G

Variant names:

• chr22-31713656-A-G
• NM_173566.3:c.4183T>C
• PRR14L p.Leu1395Leu

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_173566.3(PRR14L):​c.4183T>C​(p.Leu1395Leu) variant causes a synonymous 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. 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 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.583
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP7: Synonymous conserved (PhyloP=0.583 with no splicing effect.

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.4183T>C	p.Leu1395Leu	synonymous	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.4183T>C	p.Leu1395Leu	synonymous	Exon 4 of 9	ENSP00000331845.6	Q5THK1-1
	PRR14L	ENST00000923610.1		c.4183T>C	p.Leu1395Leu	synonymous	Exon 4 of 9	ENSP00000593669.1
	PRR14L	ENST00000923611.1		c.4183T>C	p.Leu1395Leu	synonymous	Exon 4 of 9	ENSP00000593670.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.33
PhyloP100		0.58
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr22-32109642;