rs7719971

chr5-120626881-A-Gchr5-120626881-A-T

Variant summary

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

The NM_001300783.2(PRR16):c.160-59073A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,948 control chromosomes in the GnomAD database, including 15,546 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 (15546 hom., cov: 32)
• Consequence: PRR16 NM_001300783.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRR16	NM_001300783.2	c.160-59073A>G		intron_variant		ENST00000407149.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRR16	ENST00000407149.7	c.160-59073A>G		intron_variant		1	NM_001300783.2	P1

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66629 AN: 151830 Hom.: 15522 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.439 AC: 66686 AN: 151948 Hom.: 15546 Cov.: 32 AF XY: 0.444 AC XY: 32991 AN XY: 74256

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.434

Gnomad4 EAS AF: 0.866

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.435

Alfa AF: 0.417 Hom.: 1671

Bravo AF: 0.447

Asia WGS AF: 0.630 AC: 2176 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.6
Dann	Benign	0.83

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: rs7719971; hg19: chr5-119962576;