rs13209883
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_003800.5(RNGTT):c.896+8576G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0281 in 152,316 control chromosomes in the GnomAD database, including 80 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: 𝑓 0.028 ( 80 hom., cov: 32)
Consequence
RNGTT
NM_003800.5 intron
NM_003800.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.386
Genes affected
RNGTT (HGNC:10073): (RNA guanylyltransferase and 5'-phosphatase) Enables mRNA guanylyltransferase activity and triphosphatase activity. Involved in 7-methylguanosine mRNA capping. Predicted to be located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0281 (4282/152316) while in subpopulation NFE AF= 0.0418 (2841/68018). AF 95% confidence interval is 0.0405. There are 80 homozygotes in gnomad4. There are 2004 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 80 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNGTT | NM_003800.5 | c.896+8576G>T | intron_variant | ENST00000369485.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNGTT | ENST00000369485.9 | c.896+8576G>T | intron_variant | 1 | NM_003800.5 | P1 | |||
RNGTT | ENST00000369475.7 | c.896+8576G>T | intron_variant | 1 | |||||
RNGTT | ENST00000538899.2 | c.896+8576G>T | intron_variant | 1 | |||||
RNGTT | ENST00000627296.1 | n.1048+8576G>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0281 AC: 4284AN: 152198Hom.: 80 Cov.: 32
GnomAD3 genomes
?
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0281 AC: 4282AN: 152316Hom.: 80 Cov.: 32 AF XY: 0.0269 AC XY: 2004AN XY: 74496
GnomAD4 genome
?
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4282
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32
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2004
AN XY:
74496
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42
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
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