rs2673836

chr10-87880205-G-Achr10-87880205-G-T

Variant summary

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

The NM_000314.8(PTEN):c.80-13820G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 150,870 control chromosomes in the GnomAD database, including 53,120 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 0.83 (53120 hom., cov: 28)
  • Failed GnomAD Quality Control
• Consequence: PTEN NM_000314.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTEN	NM_000314.8	c.80-13820G>A		intron_variant		ENST00000371953.8
PTEN	NM_001304717.5	c.599-13820G>A		intron_variant
PTEN	NM_001304718.2	c.-625-13820G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTEN	ENST00000371953.8	c.80-13820G>A		intron_variant		1	NM_000314.8	P1

Frequencies

GnomAD3 genomes AF: 0.834 AC: 125699 AN: 150764 Hom.: 53054 Cov.: 28

Gnomad AFR AF: 0.957

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.739

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.942

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.806

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.805

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.834 AC: 125817 AN: 150870 Hom.: 53120 Cov.: 28 AF XY: 0.840 AC XY: 61863 AN XY: 73690

Gnomad4 AFR AF: 0.958

Gnomad4 AMR AF: 0.834

Gnomad4 ASJ AF: 0.739

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.942

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.807

Alfa AF: 0.794 Hom.: 5919

Bravo AF: 0.838

Asia WGS AF: 0.962 AC: 3312 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.96
Dann	Benign	0.55

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: rs2673836; hg19: chr10-89639962;