rs17796714
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_105059.1(CARMN):n.280G>A 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 0.115 in 152,218 control chromosomes in the GnomAD database, including 1,435 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 0.11 ( 1434 hom., cov: 32)
Exomes 𝑓: 0.083 ( 1 hom. )
Consequence
CARMN
NR_105059.1 non_coding_transcript_exon
NR_105059.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.299
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=-0.82).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CARMN | NR_105059.1 | n.280G>A | non_coding_transcript_exon_variant | 2/6 | |||
CARMN | NR_105060.1 | n.235-955G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CARMN | ENST00000602315.2 | n.200-955G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.115 AC: 17482AN: 152040Hom.: 1436 Cov.: 32
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GnomAD4 exome AF: 0.0833 AC: 5AN: 60Hom.: 1 Cov.: 0 AF XY: 0.0952 AC XY: 4AN XY: 42
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GnomAD4 genome ? AF: 0.115 AC: 17497AN: 152158Hom.: 1434 Cov.: 32 AF XY: 0.118 AC XY: 8800AN XY: 74370
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ClinVar
Not reported inComputational scores
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Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at