17-59199349-A-G

Variant names:

• chr17-59199349-A-G
• rs7223491
• NM_018304.4:c.1014+1560A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018304.4(PRR11):​c.1014+1560A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 152,080 control chromosomes in the GnomAD database, including 16,249 homozygotes. 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: 𝑓 0.44 (16249 hom., cov: 32)
• Consequence: PRR11 NM_018304.4 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]

ENSG00000265303 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRR11	NM_018304.4	c.1014+1560A>G		intron_variant	Intron 9 of 9	ENST00000262293.9	NP_060774.2
PRR11	XM_024450828.2	c.1014+1560A>G		intron_variant	Intron 10 of 10		XP_024306596.1
PRR11	XM_047436387.1	c.1014+1560A>G		intron_variant	Intron 10 of 10		XP_047292343.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRR11	ENST00000262293.9	c.1014+1560A>G		intron_variant	Intron 9 of 9	1	NM_018304.4	ENSP00000262293.5
ENSG00000265303	ENST00000577660.1	c.135+1560A>G		intron_variant	Intron 2 of 2	3		ENSP00000464167.1

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66065 AN: 151962 Hom.: 16200 Cov.: 32

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.435 AC: 66176 AN: 152080 Hom.: 16249 Cov.: 32 AF XY: 0.436 AC XY: 32388 AN XY: 74340

Gnomad4 AFR AF: 0.676

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.394

Alfa AF: 0.403 Hom.: 3018

Bravo AF: 0.443

Asia WGS AF: 0.499 AC: 1733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.69

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;