rs861508
Positions:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The ENST00000662492.1(SPANXA2-OT1):n.102+81753T>C variant causes a intron, non coding transcript 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 0.81 ( 26045 hom., 26102 hem., cov: 23)
Failed GnomAD Quality Control
Consequence
SPANXA2-OT1
ENST00000662492.1 intron, non_coding_transcript
ENST00000662492.1 intron, non_coding_transcript
Scores
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.122
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPANXA2-OT1 | ENST00000662492.1 | n.102+81753T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.806 AC: 88660AN: 110053Hom.: 26049 Cov.: 23 AF XY: 0.805 AC XY: 26052AN XY: 32377
GnomAD3 genomes
?
AF:
AC:
88660
AN:
110053
Hom.:
Cov.:
23
AF XY:
AC XY:
26052
AN XY:
32377
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.806 AC: 88705AN: 110107Hom.: 26045 Cov.: 23 AF XY: 0.805 AC XY: 26102AN XY: 32441
GnomAD4 genome
?
Data not reliable, filtered out with message: InbreedingCoeff
AF:
AC:
88705
AN:
110107
Hom.:
Cov.:
23
AF XY:
AC XY:
26102
AN XY:
32441
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at