2-130656785-C-T

Variant summary

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

The NM_001277083.2(POTEJ):​c.2025C>T​(p.Asn675Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000107 in 149,676 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00011 ( 0 hom., cov: 37)
Exomes 𝑓: 0.000082 ( 1 hom. )
Failed GnomAD Quality Control

Consequence

POTEJ
NM_001277083.2 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.230
Variant links:
Genes affected
POTEJ (HGNC:37094): (POTE ankyrin domain family member J) 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=-0.55).
BP6
Variant 2-130656785-C-T is Benign according to our data. Variant chr2-130656785-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3778111.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.23 with no splicing effect.
BS2
High AC in GnomAd4 at 16 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
POTEJNM_001277083.2 linkc.2025C>T p.Asn675Asn synonymous_variant Exon 15 of 15 ENST00000409602.2 NP_001264012.1 P0CG39
POTEJXM_017004741.3 linkc.2055C>T p.Asn685Asn synonymous_variant Exon 16 of 16 XP_016860230.1
POTEJXM_017004742.2 linkc.936C>T p.Asn312Asn synonymous_variant Exon 10 of 10 XP_016860231.1
POTEJXM_017004743.3 linkc.882C>T p.Asn294Asn synonymous_variant Exon 8 of 8 XP_016860232.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
POTEJENST00000409602.2 linkc.2025C>T p.Asn675Asn synonymous_variant Exon 15 of 15 5 NM_001277083.2 ENSP00000387176.1 P0CG39

Frequencies

GnomAD3 genomes
AF:
0.000107
AC:
16
AN:
149570
Hom.:
0
Cov.:
37
show subpopulations
Gnomad AFR
AF:
0.0000508
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000397
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000738
Gnomad OTH
AF:
0.000971
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0000815
AC:
119
AN:
1459796
Hom.:
1
Cov.:
177
AF XY:
0.0000675
AC XY:
49
AN XY:
726204
show subpopulations
Gnomad4 AFR exome
AF:
0.000300
Gnomad4 AMR exome
AF:
0.0000448
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000101
Gnomad4 SAS exome
AF:
0.0000928
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000792
Gnomad4 OTH exome
AF:
0.000116
GnomAD4 genome
AF:
0.000107
AC:
16
AN:
149676
Hom.:
0
Cov.:
37
AF XY:
0.0000546
AC XY:
4
AN XY:
73198
show subpopulations
Gnomad4 AFR
AF:
0.0000507
Gnomad4 AMR
AF:
0.000397
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000738
Gnomad4 OTH
AF:
0.000962
Alfa
AF:
0.0000843
Hom.:
0

ClinVar

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

Submissions by phenotype

not provided Benign:1
Mar 01, 2025
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

POTEJ: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.55
CADD
Benign
5.2
DANN
Benign
0.92

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.

Other links and lift over

dbSNP: rs538946780; hg19: chr2-131414358; API