rs369023903
Positions:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS1
The NM_015450.3(POT1):c.9+10T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000353 in 1,445,034 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 0.00022 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000014 ( 0 hom. )
Consequence
POT1
NM_015450.3 intron
NM_015450.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.229
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 -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.76).
BP6
?
Variant 7-124897155-A-G is Benign according to our data. Variant chr7-124897155-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 475110.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000217 (33/151964) while in subpopulation AFR AF= 0.000794 (33/41556). AF 95% confidence interval is 0.00058. There are 0 homozygotes in gnomad4. There are 20 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POT1 | NM_015450.3 | c.9+10T>C | intron_variant | ENST00000357628.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POT1 | ENST00000357628.8 | c.9+10T>C | intron_variant | 2 | NM_015450.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000230 AC: 35AN: 151848Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000483 AC: 11AN: 227954Hom.: 0 AF XY: 0.0000162 AC XY: 2AN XY: 123658
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GnomAD4 exome AF: 0.0000139 AC: 18AN: 1293070Hom.: 0 Cov.: 22 AF XY: 0.00000925 AC XY: 6AN XY: 648752
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GnomAD4 genome ? AF: 0.000217 AC: 33AN: 151964Hom.: 0 Cov.: 32 AF XY: 0.000269 AC XY: 20AN XY: 74286
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Tumor predisposition syndrome 3 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at