5-120519440-G-C

Variant names:

• chr5-120519440-G-C
• rs10519636
• NM_001300783.2:c.159+54795G>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.159+54795G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 151,916 control chromosomes in the GnomAD database, including 3,681 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 0.22 (3681 hom., cov: 32)
• Consequence: PRR16 NM_001300783.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.246 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.159+54795G>C		intron	N/A	NP_001287712.1	Q569H4-1
	PRR16	NM_016644.3		c.90+38147G>C		intron	N/A	NP_057728.1	Q569H4-3
	PRR16	NM_001308087.2		c.-52+53729G>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.159+54795G>C		intron	N/A	ENSP00000385118.2	Q569H4-1
	PRR16	ENST00000379551.2	TSL:1	c.90+38147G>C		intron	N/A	ENSP00000368869.2	Q569H4-3
	PRR16	ENST00000509923.1	TSL:3	c.-52+53729G>C		intron	N/A	ENSP00000421256.1	D6RGF0

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32716 AN: 151798 Hom.: 3661 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.0427

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.216 AC: 32776 AN: 151916 Hom.: 3681 Cov.: 32 AF XY: 0.214 AC XY: 15863 AN XY: 74248

African (AFR) AF: 0.250 AC: 10341 AN: 41424

American (AMR) AF: 0.174 AC: 2664 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 823 AN: 3472

East Asian (EAS) AF: 0.0428 AC: 221 AN: 5166

South Asian (SAS) AF: 0.164 AC: 787 AN: 4812

European-Finnish (FIN) AF: 0.206 AC: 2174 AN: 10552

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15118 AN: 67910

Other (OTH) AF: 0.224 AC: 472 AN: 2106

Alfa AF: 0.111 Hom.: 199

Bravo AF: 0.213

Asia WGS AF: 0.134 AC: 466 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.61
PhyloP100		-0.69
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: rs10519636; hg19: chr5-119855135;