rs11880923

Positions:

• chr19-49618821-T-C

Variant summary

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

The NM_020719.3(PRR12):​c.5498-1531T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 151,446 control chromosomes in the GnomAD database, including 15,720 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 0.43 (15720 hom., cov: 28)
• Consequence: PRR12 NM_020719.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

Genes affected

PRR12 (HGNC:29217): (proline rich 12) This gene encodes a proline-rich protein that contains two A-T hook DNA binding domains. A chromosomal translocation and gene fusion between this gene and zinc finger, MIZ-type containing 1 (Gene ID: 57178) may underlie intellectual disability and neuropsychiatric problems in a human patient. Enriched expression of this gene in embryonic mouse brain suggests that this gene may play a role in nervous system development. [provided by RefSeq, Jul 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRR12	NM_020719.3	c.5498-1531T>C		intron_variant		ENST00000418929.7	NP_065770.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRR12	ENST00000418929.7	c.5498-1531T>C		intron_variant		5	NM_020719.3	ENSP00000394510	P1

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64710 AN: 151328 Hom.: 15683 Cov.: 28

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.428 AC: 64800 AN: 151446 Hom.: 15720 Cov.: 28 AF XY: 0.420 AC XY: 31085 AN XY: 73972

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.421

Alfa AF: 0.353 Hom.: 19469

Bravo AF: 0.447

Asia WGS AF: 0.401 AC: 1391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.27
DANN	Benign	0.40

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: rs11880923; hg19: chr19-50122078;