5-120519440-G-C

Variant names:

• chr5-120519440-G-C
• rs10519636
• NM_001300783.2:c.159+54795G>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+54795G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 151,916 control chromosomes in the GnomAD database, including 3,681 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 0.22 (3681 hom., cov: 32)
• Consequence: PRR16 NM_001300783.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691

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 (AFR) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRR16	NM_001300783.2	c.159+54795G>C		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+54795G>C		intron_variant	Intron 1 of 1	1	NM_001300783.2	ENSP00000385118.2
PRR16	ENST00000379551.2	c.90+38147G>C		intron_variant	Intron 2 of 2	1		ENSP00000368869.2
PRR16	ENST00000509923.1	c.-52+53729G>C		intron_variant	Intron 1 of 1	3		ENSP00000421256.1

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32716 AN: 151798 Hom.: 3661 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.0427

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.216 AC: 32776 AN: 151916 Hom.: 3681 Cov.: 32 AF XY: 0.214 AC XY: 15863 AN XY: 74248

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.0428

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.224

Alfa AF: 0.111 Hom.: 199

Bravo AF: 0.213

Asia WGS AF: 0.134 AC: 466 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.61

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: rs10519636; hg19: chr5-119855135;