2-130509194-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001277406.2(POTEI):​c.42G>A​(p.Val14Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000788 in 1,409,286 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00012 ( 0 hom., cov: 10)
Exomes 𝑓: 0.000079 ( 2 hom. )
Failed GnomAD Quality Control

Consequence

POTEI
NM_001277406.2 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.914
Variant links:
Genes affected
POTEI (HGNC:37093): (POTE ankyrin domain family member I) Involved in retina homeostasis. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BP6
Variant 2-130509194-C-T is Benign according to our data. Variant chr2-130509194-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2651369.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.914 with no splicing effect.
BS2
High AC in GnomAdExome4 at 111 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
POTEINM_001277406.2 linkc.42G>A p.Val14Val synonymous_variant Exon 1 of 15 ENST00000451531.7 NP_001264335.1 P0CG38
POTEINM_001371926.1 linkc.42G>A p.Val14Val synonymous_variant Exon 2 of 17 NP_001358855.1
POTEIXM_017004732.3 linkc.42G>A p.Val14Val synonymous_variant Exon 2 of 16 XP_016860221.1
POTEIXM_024453046.2 linkc.42G>A p.Val14Val synonymous_variant Exon 2 of 16 XP_024308814.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
POTEIENST00000451531.7 linkc.42G>A p.Val14Val synonymous_variant Exon 1 of 15 1 NM_001277406.2 ENSP00000392718.2 P0CG38
POTEIENST00000631234.1 linkc.42G>A p.Val14Val synonymous_variant Exon 1 of 13 2 ENSP00000486532.1 A0A0D9SFE8
POTEIENST00000652235.1 linkc.42G>A p.Val14Val synonymous_variant Exon 2 of 4 ENSP00000499032.1 A0A494C1H2

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
9
AN:
77976
Hom.:
0
Cov.:
10
FAILED QC
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00330
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000534
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000152
AC:
34
AN:
224350
Hom.:
0
AF XY:
0.000180
AC XY:
22
AN XY:
122404
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00310
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000403
Gnomad OTH exome
AF:
0.000178
GnomAD4 exome
AF:
0.0000788
AC:
111
AN:
1409286
Hom.:
2
Cov.:
29
AF XY:
0.0000812
AC XY:
57
AN XY:
701950
show subpopulations
Gnomad4 AFR exome
AF:
0.0000305
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00319
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000196
Gnomad4 OTH exome
AF:
0.000120
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.000115
AC:
9
AN:
77976
Hom.:
0
Cov.:
10
AF XY:
0.000164
AC XY:
6
AN XY:
36590
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00330
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000534
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000336
Hom.:
0

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Jul 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

POTEI: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
3.8
DANN
Benign
0.42

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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.

Other links and lift over

dbSNP: rs752197580; hg19: chr2-131266767; API