7-124823983-T-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_015450.3(POT1):āc.1884A>Cā(p.Thr628Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0059 in 1,588,362 control chromosomes in the GnomAD database, including 477 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_015450.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POT1 | NM_015450.3 | c.1884A>C | p.Thr628Thr | synonymous_variant | Exon 19 of 19 | ENST00000357628.8 | NP_056265.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0313 AC: 4752AN: 151990Hom.: 250 Cov.: 32
GnomAD3 exomes AF: 0.00806 AC: 1997AN: 247744Hom.: 101 AF XY: 0.00605 AC XY: 810AN XY: 133972
GnomAD4 exome AF: 0.00321 AC: 4607AN: 1436254Hom.: 227 Cov.: 29 AF XY: 0.00273 AC XY: 1957AN XY: 715748
GnomAD4 genome AF: 0.0313 AC: 4763AN: 152108Hom.: 250 Cov.: 32 AF XY: 0.0304 AC XY: 2259AN XY: 74372
ClinVar
Submissions by phenotype
not specified Benign:3
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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. -
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not provided Benign:1
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Hereditary cancer-predisposing syndrome Benign:1
This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Tumor predisposition syndrome 3 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at