rs6519442
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_165488.1(FAM230I):n.434A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 153,142 control chromosomes in the GnomAD database, including 5,183 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 0.25 ( 5143 hom., cov: 33)
Exomes 𝑓: 0.28 ( 40 hom. )
Consequence
FAM230I
NR_165488.1 non_coding_transcript_exon
NR_165488.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.274
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=-0.61).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM230I | NR_165488.1 | n.434A>C | non_coding_transcript_exon_variant | 6/10 | |||
FAM230I | NR_110539.2 | n.465A>C | non_coding_transcript_exon_variant | 7/12 | |||
FAM230I | NR_165489.1 | n.465A>C | non_coding_transcript_exon_variant | 7/11 | |||
FAM230I | NR_165490.1 | n.465A>C | non_coding_transcript_exon_variant | 7/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM230I | ENST00000320372.9 | n.465A>C | non_coding_transcript_exon_variant | 7/12 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.250 AC: 37990AN: 152056Hom.: 5147 Cov.: 33
GnomAD3 genomes
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GnomAD4 exome AF: 0.284 AC: 275AN: 968Hom.: 40 Cov.: 0 AF XY: 0.272 AC XY: 142AN XY: 522
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GnomAD4 genome ? AF: 0.250 AC: 37990AN: 152174Hom.: 5143 Cov.: 33 AF XY: 0.244 AC XY: 18138AN XY: 74378
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at