chr5-120601996-G-A

Position:

• chr5-120601996-G-A

Variant summary

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

The NM_001300783.2(PRR16):​c.160-83958G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0913 in 152,018 control chromosomes in the GnomAD database, including 1,359 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 0.091 (1359 hom., cov: 32)
• Consequence: PRR16 NM_001300783.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRR16	NM_001300783.2	c.160-83958G>A		intron_variant		ENST00000407149.7	NP_001287712.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRR16	ENST00000407149.7	c.160-83958G>A		intron_variant		1	NM_001300783.2	ENSP00000385118	P1
PRR16	ENST00000379551.2	c.91-83958G>A		intron_variant		1		ENSP00000368869
PRR16	ENST00000505123.5	c.-273-15099G>A		intron_variant		3		ENSP00000423446
PRR16	ENST00000509923.1	c.-51-83958G>A		intron_variant		3		ENSP00000421256

Frequencies

GnomAD3 genomes AF: 0.0911 AC: 13844 AN: 151902 Hom.: 1356 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0436

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0338

Gnomad FIN AF: 0.0493

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0260

Gnomad OTH AF: 0.0651

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

GnomAD4 genome AF: 0.0913 AC: 13875 AN: 152018 Hom.: 1359 Cov.: 32 AF XY: 0.0892 AC XY: 6633 AN XY: 74332

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.0435

Gnomad4 ASJ AF: 0.0395

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0340

Gnomad4 FIN AF: 0.0493

Gnomad4 NFE AF: 0.0260

Gnomad4 OTH AF: 0.0644

Alfa AF: 0.0348 Hom.: 272

Bravo AF: 0.0984

Asia WGS AF: 0.0250 AC: 87 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.20

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: rs1584468; hg19: chr5-119937691;