rs2304927
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_027058.1(SNHG20):n.118G>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 0.0378 in 149,106 control chromosomes in the GnomAD database, including 192 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 0.038 ( 192 hom., cov: 32)
Exomes 𝑓: 0.045 ( 0 hom. )
Consequence
SNHG20
NR_027058.1 non_coding_transcript_exon
NR_027058.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.569
Genes affected
SNHG20 (HGNC:33099): (small nucleolar RNA host gene 20)
SEC14L1 (HGNC:10698): (SEC14 like lipid binding 1) The protein encoded by this gene belongs to the SEC14 cytosolic factor family. It has similarity to yeast SEC14 and to Japanese flying squid RALBP which suggests a possible role of the gene product in an intracellular transport system. Multiple alternatively spliced transcript variants have been found for this gene; some variants represent read-through transcripts that include exons from the upstream gene C17orf86. [provided by RefSeq, Feb 2011]
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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=-1.03).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SNHG20 | NR_027058.1 | n.118G>A | non_coding_transcript_exon_variant | 1/3 | |||
SEC14L1 | NM_001204408.2 | c.-548G>A | 5_prime_UTR_variant | 1/20 | |||
SEC14L1 | NM_001204410.2 | c.-548G>A | 5_prime_UTR_variant | 1/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SNHG20 | ENST00000564414.5 | n.149-393G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0378 AC: 5629AN: 148874Hom.: 194 Cov.: 32
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GnomAD4 exome AF: 0.0446 AC: 5AN: 112Hom.: 0 Cov.: 0 AF XY: 0.0581 AC XY: 5AN XY: 86
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GnomAD4 genome ? AF: 0.0378 AC: 5629AN: 148994Hom.: 192 Cov.: 32 AF XY: 0.0381 AC XY: 2771AN XY: 72732
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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
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at