5-120543387-G-A

Variant names:

• chr5-120543387-G-A
• rs10063554
• NM_001300783.2:c.159+78742G>A

Variant summary

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

The ENST00000407149.7(PRR16):​c.159+78742G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 151,838 control chromosomes in the GnomAD database, including 3,245 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 0.20 (3245 hom., cov: 32)
• Consequence: PRR16 ENST00000407149.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000407149.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRR16	NM_001300783.2	MANE Select	c.159+78742G>A		intron	N/A	NP_001287712.1
	PRR16	NM_016644.3		c.90+62094G>A		intron	N/A	NP_057728.1
	PRR16	NM_001308087.2		c.-52+77676G>A		intron	N/A	NP_001295016.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRR16	ENST00000407149.7	TSL:1 MANE Select	c.159+78742G>A		intron	N/A	ENSP00000385118.2
	PRR16	ENST00000379551.2	TSL:1	c.90+62094G>A		intron	N/A	ENSP00000368869.2
	PRR16	ENST00000505123.5	TSL:3	c.-274+11825G>A		intron	N/A	ENSP00000423446.1

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30741 AN: 151718 Hom.: 3249 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.203 AC: 30763 AN: 151838 Hom.: 3245 Cov.: 32 AF XY: 0.206 AC XY: 15280 AN XY: 74174

African (AFR) AF: 0.193 AC: 8007 AN: 41398

American (AMR) AF: 0.153 AC: 2333 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 649 AN: 3468

East Asian (EAS) AF: 0.135 AC: 695 AN: 5160

South Asian (SAS) AF: 0.182 AC: 874 AN: 4812

European-Finnish (FIN) AF: 0.307 AC: 3234 AN: 10522

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14315 AN: 67930

Other (OTH) AF: 0.196 AC: 413 AN: 2102

Alfa AF: 0.200 Hom.: 5234

Bravo AF: 0.187

Asia WGS AF: 0.162 AC: 562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.97
DANN	Benign	0.65
PhyloP100		-0.17
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: rs10063554; hg19: chr5-119879082;