rs1150738

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr6-30067312-C-A
• chr6-30067312-C-G
• chr6-30067312-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021959.3(PPP1R11):​c.-99C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0939 in 1,280,210 control chromosomes in the GnomAD database, including 6,447 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 0.086 (649 hom., cov: 32)
  • Exomes 𝑓: 0.095 (5798 hom.)
• Consequence: PPP1R11 NM_021959.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 8 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021959.3. 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
	PPP1R11	NM_021959.3	MANE Select	c.-99C>A		5_prime_UTR	Exon 1 of 3	NP_068778.1	A2BEK1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PPP1R11	ENST00000376772.8	TSL:1 MANE Select	c.-99C>A		5_prime_UTR	Exon 1 of 3	ENSP00000365963.3	O60927
	PPP1R11	ENST00000376769.6	TSL:2	c.-330C>A		5_prime_UTR	Exon 1 of 4	ENSP00000365960.2	Q5SRK2
	PPP1R11	ENST00000376773.5	TSL:3	c.-88+303C>A		intron	N/A	ENSP00000365964.1	Q5SRK2

Frequencies

GnomAD3 genomes AF: 0.0860 AC: 13076 AN: 152110 Hom.: 647 Cov.: 32

Gnomad AFR AF: 0.0638

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0668

Gnomad EAS AF: 0.0387

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0778

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0901

Gnomad OTH AF: 0.0915

GnomAD4 exome AF: 0.0949 AC: 107062 AN: 1127984 Hom.: 5798 Cov.: 15 AF XY: 0.0960 AC XY: 54365 AN XY: 566390

African (AFR) AF: 0.0559 AC: 1486 AN: 26572

American (AMR) AF: 0.180 AC: 7073 AN: 39344

Ashkenazi Jewish (ASJ) AF: 0.0616 AC: 1349 AN: 21906

East Asian (EAS) AF: 0.0626 AC: 2305 AN: 36802

South Asian (SAS) AF: 0.138 AC: 10147 AN: 73770

European-Finnish (FIN) AF: 0.0861 AC: 4423 AN: 51364

Middle Eastern (MID) AF: 0.0597 AC: 298 AN: 4988

European-Non Finnish (NFE) AF: 0.0921 AC: 75951 AN: 824668

Other (OTH) AF: 0.0830 AC: 4030 AN: 48570

GnomAD4 genome AF: 0.0861 AC: 13100 AN: 152226 Hom.: 649 Cov.: 32 AF XY: 0.0864 AC XY: 6429 AN XY: 74430

African (AFR) AF: 0.0639 AC: 2652 AN: 41532

American (AMR) AF: 0.149 AC: 2277 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0668 AC: 232 AN: 3472

East Asian (EAS) AF: 0.0388 AC: 201 AN: 5178

South Asian (SAS) AF: 0.111 AC: 533 AN: 4820

European-Finnish (FIN) AF: 0.0778 AC: 825 AN: 10600

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.0901 AC: 6129 AN: 68016

Other (OTH) AF: 0.0905 AC: 191 AN: 2110

Alfa AF: 0.0852 Hom.: 1236

Bravo AF: 0.0907

Asia WGS AF: 0.0720 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	6.6
DANN	Benign	0.84
PhyloP100		-0.18
PromoterAI		-0.11	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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;