chr14-100882680-A-G
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_001134888.3(RTL1):āc.2109T>Cā(p.Phe703=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 1,551,690 control chromosomes in the GnomAD database, including 429,054 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.75 ( 43792 hom., cov: 31)
Exomes š: 0.74 ( 385262 hom. )
Consequence
RTL1
NM_001134888.3 synonymous
NM_001134888.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.48
Genes affected
RTL1 (HGNC:14665): (retrotransposon Gag like 1) This gene is a retrotransposon-derived, paternally expressed imprinted gene that is highly expressed at the late fetal stage in both the fetus and placenta. It has an overlapping maternally expressed antisense transcript, which contains several microRNAs targeting the transcripts of this gene through an RNA interference (RNAi) mechanism. This gene is essential for maintenance of the fetal capillaries. [provided by RefSeq, Jul 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BP7
Synonymous conserved (PhyloP=-2.48 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RTL1 | NM_001134888.3 | c.2109T>C | p.Phe703= | synonymous_variant | 4/4 | ENST00000649591.1 | |
RTL1 | XM_047431358.1 | c.2109T>C | p.Phe703= | synonymous_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RTL1 | ENST00000649591.1 | c.2109T>C | p.Phe703= | synonymous_variant | 4/4 | NM_001134888.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.751 AC: 114051AN: 151910Hom.: 43757 Cov.: 31
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GnomAD3 exomes AF: 0.665 AC: 105114AN: 158068Hom.: 36877 AF XY: 0.662 AC XY: 55282AN XY: 83474
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GnomAD4 exome AF: 0.736 AC: 1029941AN: 1399662Hom.: 385262 Cov.: 84 AF XY: 0.729 AC XY: 503462AN XY: 690324
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GnomAD4 genome AF: 0.751 AC: 114132AN: 152028Hom.: 43792 Cov.: 31 AF XY: 0.743 AC XY: 55193AN XY: 74318
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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