chr5-120590610-T-C

Position:

• chr5-120590610-T-C

Variant summary

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

The NM_001300783.2(PRR16):​c.160-95344T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.791 in 151,932 control chromosomes in the GnomAD database, including 48,022 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 0.79 (48022 hom., cov: 31)
• Consequence: PRR16 NM_001300783.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.179

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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRR16	NM_001300783.2	c.160-95344T>C		intron_variant		ENST00000407149.7	NP_001287712.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRR16	ENST00000407149.7	c.160-95344T>C		intron_variant		1	NM_001300783.2	ENSP00000385118	P1
PRR16	ENST00000379551.2	c.91-95344T>C		intron_variant		1		ENSP00000368869
PRR16	ENST00000505123.5	c.-273-26485T>C		intron_variant		3		ENSP00000423446
PRR16	ENST00000509923.1	c.-51-95344T>C		intron_variant		3		ENSP00000421256

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120161 AN: 151814 Hom.: 47995 Cov.: 31

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.880

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.689

Gnomad MID AF: 0.809

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.791 AC: 120238 AN: 151932 Hom.: 48022 Cov.: 31 AF XY: 0.788 AC XY: 58528 AN XY: 74274

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.880

Gnomad4 ASJ AF: 0.847

Gnomad4 EAS AF: 0.912

Gnomad4 SAS AF: 0.833

Gnomad4 FIN AF: 0.689

Gnomad4 NFE AF: 0.824

Gnomad4 OTH AF: 0.837

Alfa AF: 0.831 Hom.: 81309

Bravo AF: 0.803

Asia WGS AF: 0.873 AC: 3028 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.71

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: rs1037569; hg19: chr5-119926305;