rs10063554

chr5-120543387-G-A

Variant summary

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

The NM_001300783.2(PRR16):c.159+78742G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 151,838 control chromosomes in the GnomAD database, including 3,245 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 0.20 (3245 hom., cov: 32)
• Consequence: PRR16 NM_001300783.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRR16	NM_001300783.2	c.159+78742G>A		intron_variant		ENST00000407149.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRR16	ENST00000407149.7	c.159+78742G>A		intron_variant		1	NM_001300783.2	P1
PRR16	ENST00000379551.2	c.90+62094G>A		intron_variant		1
PRR16	ENST00000505123.5	c.-274+11825G>A		intron_variant		3
PRR16	ENST00000509923.1	c.-52+77676G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30741 AN: 151718 Hom.: 3249 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.203 AC: 30763 AN: 151838 Hom.: 3245 Cov.: 32 AF XY: 0.206 AC XY: 15280 AN XY: 74174

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.187

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.196

Alfa AF: 0.201 Hom.: 4170

Bravo AF: 0.187

Asia WGS AF: 0.162 AC: 562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.97
Dann	Benign	0.65

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: rs10063554; hg19: chr5-119879082;