rs210162
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_027908.2(LINC00336):n.220T>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 0.237 in 404,854 control chromosomes in the GnomAD database, including 13,344 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 0.22 ( 4047 hom., cov: 34)
Exomes 𝑓: 0.25 ( 9297 hom. )
Consequence
LINC00336
NR_027908.2 non_coding_transcript_exon
NR_027908.2 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.206
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=-0.99).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC00336 | NR_027908.2 | n.220T>C | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LINC00336 | ENST00000477984.1 | n.220T>C | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
LINC00336 | ENST00000689377.1 | n.198T>C | non_coding_transcript_exon_variant | 1/2 |
Frequencies
GnomAD3 genomes ? AF: 0.217 AC: 33039AN: 152062Hom.: 4038 Cov.: 34
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GnomAD3 exomes AF: 0.255 AC: 29084AN: 114128Hom.: 4595 AF XY: 0.268 AC XY: 15903AN XY: 59232
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GnomAD4 exome AF: 0.250 AC: 63074AN: 252674Hom.: 9297 Cov.: 0 AF XY: 0.268 AC XY: 37210AN XY: 138614
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GnomAD4 genome ? AF: 0.217 AC: 33057AN: 152180Hom.: 4047 Cov.: 34 AF XY: 0.220 AC XY: 16407AN XY: 74412
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at