rs10497171
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NR_110249.2(LINC01876):n.155-89964A>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 0.0305 in 152,262 control chromosomes in the GnomAD database, including 91 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 0.031 ( 91 hom., cov: 32)
Consequence
LINC01876
NR_110249.2 intron, non_coding_transcript
NR_110249.2 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.186
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=-0.94).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0305 (4647/152262) while in subpopulation NFE AF= 0.047 (3195/68008). AF 95% confidence interval is 0.0456. There are 91 homozygotes in gnomad4. There are 2132 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 91 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC01876 | NR_110249.2 | n.155-89964A>C | intron_variant, non_coding_transcript_variant | ||||
LINC01876 | NR_110250.2 | n.155-89933A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC01876 | ENST00000635799.1 | n.153-89964A>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0305 AC: 4646AN: 152144Hom.: 91 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: 0.0305 AC: 4647AN: 152262Hom.: 91 Cov.: 32 AF XY: 0.0286 AC XY: 2132AN XY: 74468
GnomAD4 genome
?
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4647
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152262
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32
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2132
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74468
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53
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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
Find out detailed SpliceAI scores and Pangolin per-transcript scores at