chr6-30069909-T-C

Position:

• chr6-30069909-T-C

Variant summary

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

The NM_021959.3(PPP1R11):​c.*603T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,240 control chromosomes in the GnomAD database, including 6,029 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 0.24 (6029 hom., cov: 31)
  • Exomes 𝑓: 0.095 (0 hom.)
• Consequence: PPP1R11 NM_021959.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.870

Genes affected

PPP1R11 (HGNC:9285): (protein phosphatase 1 regulatory inhibitor subunit 11) This gene encodes a specific inhibitor of protein phosphatase-1 (PP1) with a differential sensitivity toward the metal-independent and metal-dependent forms of PP1. The gene is located within the major histocompatibility complex class I region on chromosome 6. [provided by RefSeq, Jul 2008]

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 = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPP1R11	NM_021959.3	c.*603T>C		3_prime_UTR_variant	3/3	ENST00000376772.8	NP_068778.1
PPP1R11	XM_047419279.1	c.*603T>C		3_prime_UTR_variant	4/4		XP_047275235.1
PPP1R11	XM_047419280.1	c.*603T>C		3_prime_UTR_variant	5/5		XP_047275236.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP1R11	ENST00000376772.8	c.*603T>C		3_prime_UTR_variant	3/3	1	NM_021959.3	ENSP00000365963.3

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36593 AN: 151964 Hom.: 6010 Cov.: 31

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.0504

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.275

GnomAD4 exome AF: 0.0949 AC: 15 AN: 158 Hom.: 0 Cov.: 0 AF XY: 0.100 AC XY: 9 AN XY: 90

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.500

Gnomad4 FIN exome AF: 0.0500

Gnomad4 NFE exome AF: 0.0732

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.241 AC: 36651 AN: 152082 Hom.: 6029 Cov.: 31 AF XY: 0.236 AC XY: 17521 AN XY: 74344

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.0504

Gnomad4 NFE AF: 0.139

Gnomad4 OTH AF: 0.273

Alfa AF: 0.180 Hom.: 656

Bravo AF: 0.272

Asia WGS AF: 0.228 AC: 794 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	0.99
DANN	Benign	0.53
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs8347; hg19: chr6-30037686;