chr5-120590610-T-C

Variant names:

• chr5-120590610-T-C
• rs1037569
• NM_001300783.2:c.160-95344T>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.160-95344T>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
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.89 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.160-95344T>C		intron	N/A	NP_001287712.1	Q569H4-1
	PRR16	NM_016644.3		c.91-95344T>C		intron	N/A	NP_057728.1	Q569H4-3
	PRR16	NM_001308087.2		c.-51-95344T>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.160-95344T>C		intron	N/A	ENSP00000385118.2	Q569H4-1
	PRR16	ENST00000379551.2	TSL:1	c.91-95344T>C		intron	N/A	ENSP00000368869.2	Q569H4-3
	PRR16	ENST00000505123.5	TSL:3	c.-273-26485T>C		intron	N/A	ENSP00000423446.1	Q569H4-2

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

African (AFR) AF: 0.702 AC: 29083 AN: 41408

American (AMR) AF: 0.880 AC: 13422 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.847 AC: 2936 AN: 3466

East Asian (EAS) AF: 0.912 AC: 4716 AN: 5172

South Asian (SAS) AF: 0.833 AC: 4005 AN: 4808

European-Finnish (FIN) AF: 0.689 AC: 7282 AN: 10570

Middle Eastern (MID) AF: 0.808 AC: 236 AN: 292

European-Non Finnish (NFE) AF: 0.824 AC: 55975 AN: 67952

Other (OTH) AF: 0.837 AC: 1762 AN: 2104

Alfa AF: 0.822 Hom.: 183823

Bravo AF: 0.803

Asia WGS AF: 0.873 AC: 3028 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.71
PhyloP100		0.18
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: rs1037569; hg19: chr5-119926305;