rs7784168
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_015450.3(POT1):c.870-33A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 1,406,024 control chromosomes in the GnomAD database, including 72,118 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.32 ( 7704 hom., cov: 33)
Exomes 𝑓: 0.32 ( 64414 hom. )
Consequence
POT1
NM_015450.3 intron
NM_015450.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.722
Genes affected
POT1 (HGNC:17284): (protection of telomeres 1) This gene is a member of the telombin family and encodes a nuclear protein involved in telomere maintenance. Specifically, this protein functions as a member of a multi-protein complex that binds to the TTAGGG repeats of telomeres, regulating telomere length and protecting chromosome ends from illegitimate recombination, catastrophic chromosome instability, and abnormal chromosome segregation. Increased transcriptional expression of this gene is associated with stomach carcinogenesis and its progression. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jul 2008]
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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=-0.72).
BP6
?
Variant 7-124851984-T-C is Benign according to our data. Variant chr7-124851984-T-C is described in ClinVar as [Benign]. Clinvar id is 677012.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POT1 | NM_015450.3 | c.870-33A>G | intron_variant | ENST00000357628.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POT1 | ENST00000357628.8 | c.870-33A>G | intron_variant | 2 | NM_015450.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.318 AC: 48275AN: 151934Hom.: 7700 Cov.: 33
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GnomAD3 exomes AF: 0.323 AC: 75446AN: 233736Hom.: 12175 AF XY: 0.323 AC XY: 40702AN XY: 126082
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GnomAD4 exome AF: 0.317 AC: 397648AN: 1253972Hom.: 64414 Cov.: 17 AF XY: 0.319 AC XY: 201971AN XY: 633462
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GnomAD4 genome ? AF: 0.318 AC: 48306AN: 152052Hom.: 7704 Cov.: 33 AF XY: 0.319 AC XY: 23734AN XY: 74316
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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 | GeneDx | Jun 20, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
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