5-120639055-G-C

Position:

• chr5-120639055-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.160-46899G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 151,792 control chromosomes in the GnomAD database, including 14,265 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 0.42 (14265 hom., cov: 32)
• Consequence: PRR16 NM_001300783.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.835

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 = 0.84 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRR16	NM_001300783.2	c.160-46899G>C		intron_variant		ENST00000407149.7	NP_001287712.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRR16	ENST00000407149.7	c.160-46899G>C		intron_variant		1	NM_001300783.2	ENSP00000385118.2

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63315 AN: 151670 Hom.: 14244 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.300

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.417 AC: 63360 AN: 151792 Hom.: 14265 Cov.: 32 AF XY: 0.422 AC XY: 31282 AN XY: 74134

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.861

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.416

Alfa AF: 0.394 Hom.: 1516

Bravo AF: 0.428

Asia WGS AF: 0.620 AC: 2136 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.5
DANN	Benign	0.47

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: rs991672; hg19: chr5-119974750;