rs35767
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The XR_007063427(LINC02456):n.32805A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 26)
Failed GnomAD Quality Control
Consequence
LINC02456
XR_007063427 non_coding_transcript_exon
XR_007063427 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.155
Links
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LINC02456 | XR_007063427.1 | n.32805A>C | non_coding_transcript_exon_variant | 11/13 | |||
IGF1 | XM_017019259.2 | c.26T>G | p.Val9Gly | missense_variant | 1/4 | ||
IGF1 | XM_017019262.3 | c.26T>G | p.Val9Gly | missense_variant | 1/5 | ||
IGF1 | XM_017019263.3 | c.26T>G | p.Val9Gly | missense_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGF1 | ENST00000644491.1 | upstream_gene_variant | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 150182Hom.: 0 Cov.: 26 FAILED QC
GnomAD3 genomes
AF:
AC:
0
AN:
150182
Hom.:
Cov.:
26
FAILED QC
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out SpliceAI and Pangolin per-transcript scores at