5-120519026-C-A

Variant names:

• chr5-120519026-C-A
• rs1823926
• NM_001300783.2:c.159+54381C>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+54381C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 151,696 control chromosomes in the GnomAD database, including 6,793 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 0.28 (6793 hom., cov: 31)
• Consequence: PRR16 NM_001300783.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.75
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRR16	NM_001300783.2	c.159+54381C>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+54381C>A		intron_variant	Intron 1 of 1	1	NM_001300783.2	ENSP00000385118.2
PRR16	ENST00000379551.2	c.90+37733C>A		intron_variant	Intron 2 of 2	1		ENSP00000368869.2
PRR16	ENST00000509923.1	c.-52+53315C>A		intron_variant	Intron 1 of 1	3		ENSP00000421256.1

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42676 AN: 151578 Hom.: 6757 Cov.: 31

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.0430

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.282 AC: 42758 AN: 151696 Hom.: 6793 Cov.: 31 AF XY: 0.277 AC XY: 20496 AN XY: 74126

African (AFR) AF: 0.434 AC: 17918 AN: 41282

American (AMR) AF: 0.216 AC: 3294 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 850 AN: 3462

East Asian (EAS) AF: 0.0431 AC: 223 AN: 5176

South Asian (SAS) AF: 0.183 AC: 877 AN: 4802

European-Finnish (FIN) AF: 0.212 AC: 2233 AN: 10528

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.244 AC: 16576 AN: 67884

Other (OTH) AF: 0.280 AC: 591 AN: 2108

Alfa AF: 0.131 Hom.: 232

Bravo AF: 0.288

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.011
DANN	Benign	0.56
PhyloP100		-2.8
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: rs1823926; hg19: chr5-119854721; COSMIC: COSV65396600;