1-202472954-G-A

Variant names:

• chr1-202472954-G-A
• rs705736
• NM_002481.4:c.1851-15579G>A

Variant summary

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

The NM_002481.4(PPP1R12B):​c.1851-15579G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 151,940 control chromosomes in the GnomAD database, including 22,154 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 0.53 (22154 hom., cov: 32)
• Consequence: PPP1R12B NM_002481.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.105
• Publications: 2 publications found

Genes affected

PPP1R12B (HGNC:7619): (protein phosphatase 1 regulatory subunit 12B) Myosin phosphatase is a protein complex comprised of three subunits: a catalytic subunit (PP1c-delta, protein phosphatase 1, catalytic subunit delta), a large regulatory subunit (MYPT, myosin phosphatase target) and small regulatory subunit (sm-M20). Two isoforms of MYPT have been isolated--MYPT1 and MYPT2, the first of which is widely expressed, and the second of which may be specific to heart, skeletal muscle, and brain. Each of the MYPT isoforms functions to bind PP1c-delta and increase phosphatase activity. This locus encodes both MYTP2 and M20. Alternatively spliced transcript variants encoding different isoforms have been identified. Related pseudogenes have been defined on the Y chromosome. [provided by RefSeq, Oct 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP1R12B	NM_002481.4	c.1851-15579G>A		intron_variant	Intron 13 of 23	ENST00000608999.6	NP_002472.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP1R12B	ENST00000608999.6	c.1851-15579G>A		intron_variant	Intron 13 of 23	1	NM_002481.4	ENSP00000476755.1

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81143 AN: 151822 Hom.: 22124 Cov.: 32

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.707

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.535 AC: 81220 AN: 151940 Hom.: 22154 Cov.: 32 AF XY: 0.536 AC XY: 39760 AN XY: 74244

African (AFR) AF: 0.575 AC: 23811 AN: 41422

American (AMR) AF: 0.625 AC: 9539 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1333 AN: 3470

East Asian (EAS) AF: 0.707 AC: 3652 AN: 5168

South Asian (SAS) AF: 0.634 AC: 3052 AN: 4814

European-Finnish (FIN) AF: 0.467 AC: 4922 AN: 10546

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33367 AN: 67950

Other (OTH) AF: 0.507 AC: 1068 AN: 2108

Alfa AF: 0.516 Hom.: 2532

Bravo AF: 0.545

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	9.5
DANN	Benign	0.66
PhyloP100		-0.10
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: rs705736; hg19: chr1-202442082;