rs3759607
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_017924.4(C14orf119):c.-1-724A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0921 in 152,256 control chromosomes in the GnomAD database, including 838 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 0.092 ( 838 hom., cov: 31)
Consequence
C14orf119
NM_017924.4 intron
NM_017924.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.696
Genes affected
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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=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
C14orf119 | NM_017924.4 | c.-1-724A>G | intron_variant | ENST00000319074.6 | NP_060394.1 | |||
C14orf119 | XM_017021390.3 | c.-1-724A>G | intron_variant | XP_016876879.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
C14orf119 | ENST00000319074.6 | c.-1-724A>G | intron_variant | 1 | NM_017924.4 | ENSP00000322238.4 | ||||
C14orf119 | ENST00000554203.1 | c.-17-708A>G | intron_variant | 2 | ENSP00000450861.1 |
Frequencies
GnomAD3 genomes AF: 0.0920 AC: 13995AN: 152138Hom.: 832 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0921 AC: 14024AN: 152256Hom.: 838 Cov.: 31 AF XY: 0.0917 AC XY: 6831AN XY: 74460
GnomAD4 genome
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459
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3478
ClinVar
Not reported inComputational scores
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Name
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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