rs300962

Positions:

• chr5-120546248-G-A
• chr5-120546248-G-C

Variant summary

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

The NM_001300783.2(PRR16):​c.159+81603G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 151,834 control chromosomes in the GnomAD database, including 38,295 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 0.70 (38295 hom., cov: 31)
• Consequence: PRR16 NM_001300783.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353

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=-0.9).
• 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.159+81603G>A		intron_variant		ENST00000407149.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRR16	ENST00000407149.7	c.159+81603G>A		intron_variant		1	NM_001300783.2	P1
PRR16	ENST00000379551.2	c.90+64955G>A		intron_variant		1
PRR16	ENST00000505123.5	c.-274+14686G>A		intron_variant		3
PRR16	ENST00000509923.1	c.-52+80537G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.705 AC: 106970 AN: 151716 Hom.: 38269 Cov.: 31

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.760

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.743

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.705 AC: 107040 AN: 151834 Hom.: 38295 Cov.: 31 AF XY: 0.704 AC XY: 52260 AN XY: 74186

Gnomad4 AFR AF: 0.587

Gnomad4 AMR AF: 0.803

Gnomad4 ASJ AF: 0.760

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.743

Gnomad4 OTH AF: 0.729

Alfa AF: 0.739 Hom.: 22361

Bravo AF: 0.714

Asia WGS AF: 0.806 AC: 2805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.55
DANN	Benign	0.26

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: rs300962; hg19: chr5-119881943;