rs7223491

Positions:

• chr17-59199349-A-C
• chr17-59199349-A-G
• chr17-59199349-A-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000262293.9(PRR11):​c.1014+1560A>C variant causes a intron 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: PRR11 ENST00000262293.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227

Genes affected

PRR11 (HGNC:25619): (proline rich 11) Involved in regulation of cell cycle. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRR11	NM_018304.4	c.1014+1560A>C		intron_variant		ENST00000262293.9	NP_060774.2
PRR11	XM_024450828.2	c.1014+1560A>C		intron_variant			XP_024306596.1
PRR11	XM_047436387.1	c.1014+1560A>C		intron_variant			XP_047292343.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRR11	ENST00000262293.9	c.1014+1560A>C		intron_variant		1	NM_018304.4	ENSP00000262293	P1
PRR11	ENST00000614081.1	c.1014+1560A>C		intron_variant		1		ENSP00000481852	P1
PRR11	ENST00000580177.5	c.1014+1560A>C		intron_variant, NMD_transcript_variant		1		ENSP00000463733
PRR11	ENST00000578542.5	c.1014+1560A>C		intron_variant, NMD_transcript_variant		5		ENSP00000464171

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.67

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

Publications

LitVar

Other links and lift over

dbSNP: rs7223491; hg19: chr17-57276710;