5-120639055-G-C

Variant names:

• chr5-120639055-G-C
• rs991672
• NM_001300783.2:c.160-46899G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001300783.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRR16	NM_001300783.2	MANE Select	c.160-46899G>C		intron	N/A	NP_001287712.1	Q569H4-1
	PRR16	NM_016644.3		c.91-46899G>C		intron	N/A	NP_057728.1	Q569H4-3
	PRR16	NM_001308087.2		c.-51-46899G>C		intron	N/A	NP_001295016.1	Q569H4-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRR16	ENST00000407149.7	TSL:1 MANE Select	c.160-46899G>C		intron	N/A	ENSP00000385118.2	Q569H4-1
	PRR16	ENST00000379551.2	TSL:1	c.91-46899G>C		intron	N/A	ENSP00000368869.2	Q569H4-3
	PRR16	ENST00000446965.2	TSL:1	c.-1+20490G>C		intron	N/A	ENSP00000405491.2	A0A0A0MSW7

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

African (AFR) AF: 0.316 AC: 13094 AN: 41412

American (AMR) AF: 0.536 AC: 8145 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1495 AN: 3466

East Asian (EAS) AF: 0.861 AC: 4432 AN: 5146

South Asian (SAS) AF: 0.452 AC: 2180 AN: 4822

European-Finnish (FIN) AF: 0.421 AC: 4437 AN: 10532

Middle Eastern (MID) AF: 0.309 AC: 87 AN: 282

European-Non Finnish (NFE) AF: 0.415 AC: 28152 AN: 67916

Other (OTH) AF: 0.416 AC: 876 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.5
DANN	Benign	0.47
PhyloP100		0.83
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: rs991672; hg19: chr5-119974750;