rs10517377
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_122079.1(LOC439933):n.361-5557A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 152,214 control chromosomes in the GnomAD database, including 2,993 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 0.18 ( 2993 hom., cov: 32)
Consequence
LOC439933
NR_122079.1 intron, non_coding_transcript
NR_122079.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.33
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=-0.93).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC439933 | NR_122079.1 | n.361-5557A>C | intron_variant, non_coding_transcript_variant | ||||
LOC439933 | NR_122080.1 | n.338-5845A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000499292.2 | n.361-5557A>C | intron_variant, non_coding_transcript_variant | 1 | ||||||
ENST00000502245.2 | n.386-5845A>C | intron_variant, non_coding_transcript_variant | 1 | ||||||
ENST00000691596.1 | n.193-5845A>C | intron_variant, non_coding_transcript_variant | |||||||
ENST00000692213.1 | n.193-5557A>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.180 AC: 27428AN: 152096Hom.: 2992 Cov.: 32
GnomAD3 genomes
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32
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GnomAD4 genome ? AF: 0.180 AC: 27428AN: 152214Hom.: 2993 Cov.: 32 AF XY: 0.178 AC XY: 13241AN XY: 74404
GnomAD4 genome
?
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27428
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32
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13241
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74404
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495
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at