2-27377381-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_144631.6(ZNF513):c.*164G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ZNF513
NM_144631.6 3_prime_UTR
NM_144631.6 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.25
Publications
0 publications found
Genes affected
ZNF513 (HGNC:26498): (zinc finger protein 513) The protein encoded by this gene is a possible transcriptional regulator involved in retinal development. Defects in this gene can be a cause of autosomal-recessive retinitis pigmentosa. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2011]
SNX17 (HGNC:14979): (sorting nexin 17) This gene encodes a member of the sorting nexin family. Members of this family contain a phox (PX) domain, which is a phosphoinositide binding domain, and are involved in intracellular trafficking. This protein does not contain a coiled coil region, like some family members, but contains a B41 domain. This protein interacts with the cytoplasmic domain of P-selectin, and may function in the intracellular trafficking of P-selectin. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2012]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_144631.6. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| ZNF513 | TSL:1 MANE Select | c.*164G>A | 3_prime_UTR | Exon 4 of 4 | ENSP00000318373.6 | Q8N8E2-1 | |||
| SNX17 | TSL:1 MANE Select | c.*662C>T | 3_prime_UTR | Exon 15 of 15 | ENSP00000233575.2 | Q15036-1 | |||
| ZNF513 | TSL:1 | c.*164G>A | 3_prime_UTR | Exon 3 of 3 | ENSP00000384874.1 | Q8N8E2-2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 626512Hom.: 0 Cov.: 8 AF XY: 0.00 AC XY: 0AN XY: 334626
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
626512
Hom.:
Cov.:
8
AF XY:
AC XY:
0
AN XY:
334626
African (AFR)
AF:
AC:
0
AN:
17146
American (AMR)
AF:
AC:
0
AN:
34836
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
20464
East Asian (EAS)
AF:
AC:
0
AN:
32518
South Asian (SAS)
AF:
AC:
0
AN:
63556
European-Finnish (FIN)
AF:
AC:
0
AN:
33786
Middle Eastern (MID)
AF:
AC:
0
AN:
4216
European-Non Finnish (NFE)
AF:
AC:
0
AN:
386922
Other (OTH)
AF:
AC:
0
AN:
33068
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
Retinitis pigmentosa (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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