rs2299941

chr10-87944962-A-G

Variant summary

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

The NM_000314.8(PTEN):c.493-7156A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,280 control chromosomes in the GnomAD database, including 1,071 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 0.10 (1071 hom., cov: 32)
• Consequence: PTEN NM_000314.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.156

Genes affected

PTEN (HGNC:9588): (phosphatase and tensin homolog) This gene was identified as a tumor suppressor that is mutated in a large number of cancers at high frequency. The protein encoded by this gene is a phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase. It contains a tensin like domain as well as a catalytic domain similar to that of the dual specificity protein tyrosine phosphatases. Unlike most of the protein tyrosine phosphatases, this protein preferentially dephosphorylates phosphoinositide substrates. It negatively regulates intracellular levels of phosphatidylinositol-3,4,5-trisphosphate in cells and functions as a tumor suppressor by negatively regulating AKT/PKB signaling pathway. The use of a non-canonical (CUG) upstream initiation site produces a longer isoform that initiates translation with a leucine, and is thought to be preferentially associated with the mitochondrial inner membrane. This longer isoform may help regulate energy metabolism in the mitochondria. A pseudogene of this gene is found on chromosome 9. Alternative splicing and the use of multiple translation start codons results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Feb 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTEN	NM_000314.8	c.493-7156A>G		intron_variant		ENST00000371953.8
PTEN	NM_001304717.5	c.1012-7156A>G		intron_variant
PTEN	NM_001304718.2	c.-99+2193A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTEN	ENST00000371953.8	c.493-7156A>G		intron_variant		1	NM_000314.8	P1

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15279 AN: 152162 Hom.: 1072 Cov.: 32

Gnomad AFR AF: 0.0252

Gnomad AMI AF: 0.0560

Gnomad AMR AF: 0.0985

Gnomad ASJ AF: 0.0916

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0937

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.0880

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

GnomAD4 genome AF: 0.100 AC: 15273 AN: 152280 Hom.: 1071 Cov.: 32 AF XY: 0.0995 AC XY: 7409 AN XY: 74456

Gnomad4 AFR AF: 0.0251

Gnomad4 AMR AF: 0.0985

Gnomad4 ASJ AF: 0.0916

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0937

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.0871

Alfa AF: 0.111 Hom.: 201

Bravo AF: 0.0985

Asia WGS AF: 0.197 AC: 684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.48
Dann	Benign	0.63

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: rs2299941; hg19: chr10-89704719;