chr10-87895479-A-G

Position:

• chr10-87895479-A-G

Variant summary

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

The ENST00000371953.8(PTEN):​c.164+1370A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 130,446 control chromosomes in the GnomAD database, including 1,509 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 0.15 (1509 hom., cov: 31)
• Consequence: PTEN ENST00000371953.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.728

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTEN	NM_000314.8	c.164+1370A>G		intron_variant		ENST00000371953.8	NP_000305.3
PTEN	NM_001304717.5	c.683+1370A>G		intron_variant			NP_001291646.4
PTEN	NM_001304718.2	c.-541+1370A>G		intron_variant			NP_001291647.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTEN	ENST00000371953.8	c.164+1370A>G		intron_variant		1	NM_000314.8	ENSP00000361021	P1

Frequencies

GnomAD3 genomes AF: 0.147 AC: 19157 AN: 130336 Hom.: 1507 Cov.: 31

Gnomad AFR AF: 0.0642

Gnomad AMI AF: 0.0808

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.147 AC: 19170 AN: 130446 Hom.: 1509 Cov.: 31 AF XY: 0.149 AC XY: 9412 AN XY: 63102

Gnomad4 AFR AF: 0.0644

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.158

Alfa AF: 0.134 Hom.: 161

Bravo AF: 0.132

Asia WGS AF: 0.229 AC: 764 AN: 3338

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.1
DANN	Benign	0.80

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: rs10887763; hg19: chr10-89655236;