Variant 14-19424250-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_001005356.3(POTEG):c.970C>G(p.Leu324Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000088 ( 0 hom., cov: 29)

Exomes 𝑓: 0.0000055 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

POTEG
NM_001005356.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.46

Variant links:

Genes affected

POTEG (HGNC:33896): (POTE ankyrin domain family member G)

POTEG links:

(HGNC:):

links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
POTEG	NM_001005356.3 linkuse as main transcript	c.970C>G	p.Leu324Val	missense_variant	5/11	ENST00000547848.5
LOC101929572	NR_110504.1 linkuse as main transcript	n.1748G>C		non_coding_transcript_exon_variant	2/2
POTEG	NR_027480.2 linkuse as main transcript	n.1022C>G		non_coding_transcript_exon_variant	5/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POTEG	ENST00000547848.5 linkuse as main transcript	c.970C>G	p.Leu324Val	missense_variant	5/11	1	NM_001005356.3	P1	Q6S5H5-3
	ENST00000621705.1 linkuse as main transcript	n.1799G>C		non_coding_transcript_exon_variant	2/2	1
POTEG	ENST00000622767.4 linkuse as main transcript	c.970C>G	p.Leu324Val	missense_variant, NMD_transcript_variant	5/12	1			Q6S5H5-2
POTEG	ENST00000547722.1 linkuse as main transcript	c.*257C>G		3_prime_UTR_variant, NMD_transcript_variant	6/12	2			Q6S5H5-4

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

147282

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.000335

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00000555

AC:

AN:

1441652

Hom.:

Cov.:

AF XY:

0.00000558

AC XY:

AN XY:

717488

show subpopulations

Gnomad4 AFR exome

AF:

0.000125

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000182

Gnomad4 OTH exome

AF:

0.0000336

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000883

AC:

AN:

147282

Hom.:

Cov.:

AF XY:

0.0000837

AC XY:

AN XY:

71710

show subpopulations

Gnomad4 AFR

AF:

0.000335

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jan 23, 2023

The c.970C>G (p.L324V) alteration is located in exon 5 (coding exon 5) of the POTEG gene. This alteration results from a C to G substitution at nucleotide position 970, causing the leucine (L) at amino acid position 324 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.42

BayesDel_addAF

Uncertain

0.047

BayesDel_noAF

Benign

-0.17

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.057

Eigen

Benign

-0.0089

Eigen_PC

Benign

-0.30

FATHMM_MKL

Benign

0.30

LIST_S2

Benign

0.70

M_CAP

Benign

0.013

MetaRNN

Uncertain

0.72

MetaSVM

Benign

-0.31

MutationTaster

Benign

1.0

PrimateAI

Pathogenic

0.87

PROVEAN

Benign

-1.6

Sift

Benign

0.043

Sift4G

Uncertain

0.019

Vest4

0.64

MutPred

0.59

Gain of catalytic residue at S319 (P = 0);

MVP

0.67

ClinPred

0.60

GERP RS

0.91

Varity_R

0.064

gMVP

0.067

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over