chr15-76381444-G-T
Position:
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_020843.4(SCAPER):c.3639C>A(p.Ile1213=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00466 in 1,613,840 control chromosomes in the GnomAD database, including 322 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.025 ( 156 hom., cov: 32)
Exomes 𝑓: 0.0025 ( 166 hom. )
Consequence
SCAPER
NM_020843.4 synonymous
NM_020843.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.23
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
Variant 15-76381444-G-T is Benign according to our data. Variant chr15-76381444-G-T is described in ClinVar as [Benign]. Clinvar id is 776933.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=2.23 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0866 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCAPER | NM_020843.4 | c.3639C>A | p.Ile1213= | synonymous_variant | 28/32 | ENST00000563290.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCAPER | ENST00000563290.6 | c.3639C>A | p.Ile1213= | synonymous_variant | 28/32 | 5 | NM_020843.4 | P1 | |
SCAPER | ENST00000324767.11 | c.3639C>A | p.Ile1213= | synonymous_variant | 27/31 | 1 | P1 | ||
SCAPER | ENST00000538941.6 | c.2901C>A | p.Ile967= | synonymous_variant | 28/32 | 1 | |||
SCAPER | ENST00000303521.10 | n.3703C>A | non_coding_transcript_exon_variant | 27/27 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0252 AC: 3827AN: 152140Hom.: 156 Cov.: 32
GnomAD3 genomes
AF:
AC:
3827
AN:
152140
Hom.:
Cov.:
32
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:
GnomAD3 exomes AF: 0.00606 AC: 1507AN: 248862Hom.: 66 AF XY: 0.00452 AC XY: 610AN XY: 134986
GnomAD3 exomes
AF:
AC:
1507
AN:
248862
Hom.:
AF XY:
AC XY:
610
AN XY:
134986
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00252 AC: 3682AN: 1461582Hom.: 166 Cov.: 32 AF XY: 0.00211 AC XY: 1534AN XY: 727068
GnomAD4 exome
AF:
AC:
3682
AN:
1461582
Hom.:
Cov.:
32
AF XY:
AC XY:
1534
AN XY:
727068
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0252 AC: 3835AN: 152258Hom.: 156 Cov.: 32 AF XY: 0.0246 AC XY: 1829AN XY: 74440
GnomAD4 genome
AF:
AC:
3835
AN:
152258
Hom.:
Cov.:
32
AF XY:
AC XY:
1829
AN XY:
74440
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:
Asia WGS
AF:
AC:
15
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
SCAPER-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 16, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at