2-130656785-C-T
Variant names:
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
NM_001277083.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.230
Genes affected
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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 |
---|---|---|---|---|---|---|---|---|
POTEJ | NM_001277083.2 | c.2025C>T | p.Asn675Asn | synonymous_variant | Exon 15 of 15 | ENST00000409602.2 | NP_001264012.1 | |
POTEJ | XM_017004741.3 | c.2055C>T | p.Asn685Asn | synonymous_variant | Exon 16 of 16 | XP_016860230.1 | ||
POTEJ | XM_017004742.2 | c.936C>T | p.Asn312Asn | synonymous_variant | Exon 10 of 10 | XP_016860231.1 | ||
POTEJ | XM_017004743.3 | c.882C>T | p.Asn294Asn | synonymous_variant | Exon 8 of 8 | XP_016860232.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000107 AC: 16AN: 149570Hom.: 0 Cov.: 37
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000815 AC: 119AN: 1459796Hom.: 1 Cov.: 177 AF XY: 0.0000675 AC XY: 49AN XY: 726204
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome AF: 0.000107 AC: 16AN: 149676Hom.: 0 Cov.: 37 AF XY: 0.0000546 AC XY: 4AN XY: 73198
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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
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at