chr6-42246553-A-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001395490.1(TRERF1):c.2657-9T>G variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00145 in 1,591,362 control chromosomes in the GnomAD database, including 46 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0026 ( 8 hom., cov: 32)
Exomes 𝑓: 0.0013 ( 38 hom. )
Consequence
TRERF1
NM_001395490.1 splice_polypyrimidine_tract, intron
NM_001395490.1 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.07170
2
Clinical Significance
Conservation
PhyloP100: 1.73
Genes affected
TRERF1 (HGNC:18273): (transcriptional regulating factor 1) This gene encodes a zinc-finger transcriptional regulating protein which interacts with CBP/p300 to regulate the human gene CYP11A1. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.55).
BP6
?
Variant 6-42246553-A-C is Benign according to our data. Variant chr6-42246553-A-C is described in ClinVar as [Benign]. Clinvar id is 779911.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00263 (401/152320) while in subpopulation EAS AF= 0.022 (114/5188). AF 95% confidence interval is 0.0187. There are 8 homozygotes in gnomad4. There are 201 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 399 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRERF1 | NM_001395490.1 | c.2657-9T>G | splice_polypyrimidine_tract_variant, intron_variant | ENST00000695948.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRERF1 | ENST00000695948.1 | c.2657-9T>G | splice_polypyrimidine_tract_variant, intron_variant | NM_001395490.1 |
Frequencies
GnomAD3 genomes ? AF: 0.00262 AC: 399AN: 152202Hom.: 8 Cov.: 32
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GnomAD3 exomes AF: 0.00610 AC: 1411AN: 231484Hom.: 30 AF XY: 0.00460 AC XY: 577AN XY: 125346
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GnomAD4 exome AF: 0.00132 AC: 1902AN: 1439042Hom.: 38 Cov.: 27 AF XY: 0.00110 AC XY: 791AN XY: 715862
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at