rs2070830

Positions:

• chr19-45386392-C-A
• chr19-45386392-C-G

Variant summary

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

The NM_006663.4(PPP1R13L):​c.1816-212G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0233 in 152,220 control chromosomes in the GnomAD database, including 239 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 0.023 (239 hom., cov: 32)
• Consequence: PPP1R13L NM_006663.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144

Genes affected

PPP1R13L (HGNC:18838): (protein phosphatase 1 regulatory subunit 13 like) IASPP is one of the most evolutionarily conserved inhibitors of p53 (TP53; MIM 191170), whereas ASPP1 (MIM 606455) and ASPP2 (MIM 602143) are activators of p53.[supplied by OMIM, Mar 2008]

PPP1R13L (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PPP1R13L	NM_006663.4	c.1816-212G>T		intron_variant		ENST00000360957.10	NP_006654.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PPP1R13L	ENST00000360957.10	c.1816-212G>T		intron_variant		1	NM_006663.4	ENSP00000354218.4
PPP1R13L	ENST00000418234.6	c.1816-212G>T		intron_variant		1		ENSP00000403902.1
PPP1R13L	ENST00000587270.5	n.1289-212G>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.0233 AC: 3550 AN: 152102 Hom.: 236 Cov.: 32

Gnomad AFR AF: 0.00193

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0890

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.0383

Gnomad FIN AF: 0.0383

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00257

Gnomad OTH AF: 0.0210

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

GnomAD4 genome AF: 0.0233 AC: 3551 AN: 152220 Hom.: 239 Cov.: 32 AF XY: 0.0276 AC XY: 2051 AN XY: 74424

Gnomad4 AFR AF: 0.00193

Gnomad4 AMR AF: 0.0895

Gnomad4 ASJ AF: 0.00807

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.0377

Gnomad4 FIN AF: 0.0383

Gnomad4 NFE AF: 0.00257

Gnomad4 OTH AF: 0.0194

Alfa AF: 0.0160 Hom.: 19

Bravo AF: 0.0295

Asia WGS AF: 0.123 AC: 428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.42

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: rs2070830; hg19: chr19-45889650;