chr3-10293461-T-C
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000662597.1(GHRLOS):n.1544T>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 0.316 in 152,118 control chromosomes in the GnomAD database, including 8,267 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 0.32 ( 8266 hom., cov: 32)
Exomes 𝑓: 0.38 ( 1 hom. )
Consequence
GHRLOS
ENST00000662597.1 non_coding_transcript_exon
ENST00000662597.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.271
Genes affected
GHRLOS (HGNC:33885): (ghrelin opposite strand/antisense RNA) This gene is an antisense gene of the ghrelin/obestatin prepropeptide gene. Alternatively spliced transcript variants have been identified and they may function as non-coding regulatory RNAs. [provided by RefSeq, Jan 2013]
SEC13 (HGNC:10697): (SEC13 homolog, nuclear pore and COPII coat complex component) The protein encoded by this gene belongs to the SEC13 family of WD-repeat proteins. It is a constituent of the endoplasmic reticulum and the nuclear pore complex. It has similarity to the yeast SEC13 protein, which is required for vesicle biogenesis from endoplasmic reticulum during the transport of proteins. Multiple alternatively spliced transcript variants have been found. [provided by RefSeq, Oct 2008]
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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=-0.9).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GHRLOS | NR_024145.2 | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GHRLOS | ENST00000662597.1 | n.1544T>C | non_coding_transcript_exon_variant | 2/2 | |||||
SEC13 | ENST00000492602.5 | n.188-125A>G | intron_variant, non_coding_transcript_variant | 3 | |||||
GHRLOS | ENST00000439539.3 | downstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.316 AC: 48018AN: 151984Hom.: 8256 Cov.: 32
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GnomAD4 exome AF: 0.375 AC: 6AN: 16Hom.: 1 Cov.: 0 AF XY: 0.250 AC XY: 2AN XY: 8
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GnomAD4 genome ? AF: 0.316 AC: 48071AN: 152102Hom.: 8266 Cov.: 32 AF XY: 0.326 AC XY: 24258AN XY: 74358
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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
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at