5-120546248-G-A

Variant names:

• chr5-120546248-G-A
• rs300962
• NM_001300783.2:c.159+81603G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PRR16	NM_001300783.2	c.159+81603G>A		intron_variant	Intron 1 of 1	ENST00000407149.7	NP_001287712.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRR16	ENST00000407149.7	c.159+81603G>A		intron_variant	Intron 1 of 1	1	NM_001300783.2	ENSP00000385118.2
PRR16	ENST00000379551.2	c.90+64955G>A		intron_variant	Intron 2 of 2	1		ENSP00000368869.2
PRR16	ENST00000505123.5	c.-274+14686G>A		intron_variant	Intron 1 of 3	3		ENSP00000423446.1
PRR16	ENST00000509923.1	c.-52+80537G>A		intron_variant	Intron 1 of 1	3		ENSP00000421256.1

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

African (AFR) AF: 0.587 AC: 24288 AN: 41410

American (AMR) AF: 0.803 AC: 12247 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.760 AC: 2635 AN: 3468

East Asian (EAS) AF: 0.865 AC: 4441 AN: 5132

South Asian (SAS) AF: 0.764 AC: 3673 AN: 4810

European-Finnish (FIN) AF: 0.653 AC: 6890 AN: 10556

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.743 AC: 50423 AN: 67900

Other (OTH) AF: 0.729 AC: 1537 AN: 2108

Alfa AF: 0.737 Hom.: 30290

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
PhyloP100		-0.35
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs300962; hg19: chr5-119881943;