rs2307733

Variant names:

• chr14-103845237-G-GATAC
• rs2307733
• NM_015316.3:c.9+2061_9+2062insGTAT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_015316.3(PPP1R13B):​c.9+2061_9+2062insGTAT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.67 (34697 hom., cov: 0)
• Consequence: PPP1R13B NM_015316.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235

Genes affected

PPP1R13B (HGNC:14950): (protein phosphatase 1 regulatory subunit 13B) This gene encodes a member of the ASPP (apoptosis-stimulating protein of p53) family of p53 interacting proteins. The protein contains four ankyrin repeats and an SH3 domain involved in protein-protein interactions. ASPP proteins are required for the induction of apoptosis by p53-family proteins. They promote DNA binding and transactivation of p53-family proteins on the promoters of proapoptotic genes. Expression of this gene is regulated by the E2F transcription factor. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PPP1R13B	NM_015316.3	c.9+2061_9+2062insGTAT		intron_variant	Intron 1 of 16	ENST00000202556.14	NP_056131.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PPP1R13B	ENST00000202556.14	c.9+2061_9+2062insGTAT		intron_variant	Intron 1 of 16	1	NM_015316.3	ENSP00000202556.9

Frequencies

GnomAD3 genomes AF: 0.666 AC: 100825 AN: 151432 Hom.: 34628 Cov.: 0

Gnomad AFR AF: 0.860

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.666 AC: 100952 AN: 151550 Hom.: 34697 Cov.: 0 AF XY: 0.662 AC XY: 49030 AN XY: 74024

Gnomad4 AFR AF: 0.860

Gnomad4 AMR AF: 0.657

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.593

Gnomad4 OTH AF: 0.614

Alfa AF: 0.644 Hom.: 3914

Bravo AF: 0.678

Asia WGS AF: 0.547 AC: 1893 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2307733; hg19: chr14-104311574;