NM_001300783.2:c.160-59073A>G

Variant names:

• chr5-120626881-A-G
• rs7719971
• NM_001300783.2:c.160-59073A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001300783.2(PRR16):​c.160-59073A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,948 control chromosomes in the GnomAD database, including 15,546 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 0.44 (15546 hom., cov: 32)
• Consequence: PRR16 NM_001300783.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 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.160-59073A>G		intron	N/A	NP_001287712.1	Q569H4-1
	PRR16	NM_016644.3		c.91-59073A>G		intron	N/A	NP_057728.1	Q569H4-3
	PRR16	NM_001308087.2		c.-51-59073A>G		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.160-59073A>G		intron	N/A	ENSP00000385118.2	Q569H4-1
	PRR16	ENST00000379551.2	TSL:1	c.91-59073A>G		intron	N/A	ENSP00000368869.2	Q569H4-3
	PRR16	ENST00000446965.2	TSL:1	c.-1+8316A>G		intron	N/A	ENSP00000405491.2	A0A0A0MSW7

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66629 AN: 151830 Hom.: 15522 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.866

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.439 AC: 66686 AN: 151948 Hom.: 15546 Cov.: 32 AF XY: 0.444 AC XY: 32991 AN XY: 74256

African (AFR) AF: 0.356 AC: 14749 AN: 41486

American (AMR) AF: 0.548 AC: 8350 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1505 AN: 3470

East Asian (EAS) AF: 0.866 AC: 4470 AN: 5164

South Asian (SAS) AF: 0.478 AC: 2304 AN: 4818

European-Finnish (FIN) AF: 0.446 AC: 4708 AN: 10550

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.428 AC: 29080 AN: 67902

Other (OTH) AF: 0.435 AC: 914 AN: 2102

Alfa AF: 0.415 Hom.: 1722

Bravo AF: 0.447

Asia WGS AF: 0.630 AC: 2176 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.83
PhyloP100		-0.44
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: rs7719971; hg19: chr5-119962576;