6-30067312-C-G

Variant names:

• chr6-30067312-C-G
• rs1150738
• NM_021959.3:c.-99C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_021959.3(PPP1R11):​c.-99C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000177 in 1,129,106 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000018 (0 hom.)
• Consequence: PPP1R11 NM_021959.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 0 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP1R11	NM_021959.3	c.-99C>G		5_prime_UTR_variant	Exon 1 of 3	ENST00000376772.8	NP_068778.1
PPP1R11	XM_047419279.1	c.-99C>G		5_prime_UTR_variant	Exon 2 of 4		XP_047275235.1
PPP1R11	XM_047419280.1	c.-99C>G		5_prime_UTR_variant	Exon 3 of 5		XP_047275236.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP1R11	ENST00000376772.8	c.-99C>G		5_prime_UTR_variant	Exon 1 of 3	1	NM_021959.3	ENSP00000365963.3
PPP1R11	ENST00000376769.6	c.-330C>G		5_prime_UTR_variant	Exon 1 of 4	2		ENSP00000365960.2
PPP1R11	ENST00000376773.5	c.-88+303C>G		intron_variant	Intron 1 of 2	3		ENSP00000365964.1
PPP1R11	ENST00000376765.6	c.-515C>G		upstream_gene_variant		3		ENSP00000365956.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000177 AC: 2 AN: 1129106 Hom.: 0 Cov.: 15 AF XY: 0.00000176 AC XY: 1 AN XY: 566922

African (AFR) AF: 0.00 AC: 0 AN: 26596

American (AMR) AF: 0.0000507 AC: 2 AN: 39410

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21916

East Asian (EAS) AF: 0.00 AC: 0 AN: 36808

South Asian (SAS) AF: 0.00 AC: 0 AN: 73852

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51398

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4992

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 825530

Other (OTH) AF: 0.00 AC: 0 AN: 48604

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	6.3
DANN	Benign	0.79
PhyloP100		-0.18
PromoterAI		-0.0039	Neutral
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

Other links and lift over

dbSNP: rs1150738; hg19: chr6-30035089;