rs75656086
Positions:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001378213.1(BCL9L):c.1272C>T(p.Ser424=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0121 in 1,608,966 control chromosomes in the GnomAD database, including 416 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.016 ( 63 hom., cov: 33)
Exomes 𝑓: 0.012 ( 353 hom. )
Consequence
BCL9L
NM_001378213.1 synonymous
NM_001378213.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.87
Genes affected
BCL9L (HGNC:23688): (BCL9 like) Enables beta-catenin binding activity. Involved in several processes, including negative regulation of transforming growth factor beta receptor signaling pathway; positive regulation of epithelial to mesenchymal transition; and positive regulation of transcription by RNA polymerase II. Located in nucleolus and nucleoplasm. Part of beta-catenin-TCF complex. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 11-118902471-G-A is Benign according to our data. Variant chr11-118902471-G-A is described in ClinVar as [Benign]. Clinvar id is 402418.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-2.87 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCL9L | NM_001378213.1 | c.1272C>T | p.Ser424= | synonymous_variant | 8/10 | ENST00000683865.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCL9L | ENST00000683865.1 | c.1272C>T | p.Ser424= | synonymous_variant | 8/10 | NM_001378213.1 | P4 | ||
BCL9L | ENST00000334801.7 | c.1272C>T | p.Ser424= | synonymous_variant | 6/8 | 1 | P4 | ||
BCL9L | ENST00000526143.2 | c.1161C>T | p.Ser387= | synonymous_variant | 6/8 | 5 | A1 | ||
BCL9L | ENST00000530293.1 | n.41-1710C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0164 AC: 2491AN: 152214Hom.: 63 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
2491
AN:
152214
Hom.:
Cov.:
33
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: 0.0204 AC: 4940AN: 242632Hom.: 205 AF XY: 0.0198 AC XY: 2617AN XY: 132380
GnomAD3 exomes
AF:
AC:
4940
AN:
242632
Hom.:
AF XY:
AC XY:
2617
AN XY:
132380
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: 0.0117 AC: 17022AN: 1456634Hom.: 353 Cov.: 41 AF XY: 0.0119 AC XY: 8603AN XY: 724606
GnomAD4 exome
AF:
AC:
17022
AN:
1456634
Hom.:
Cov.:
41
AF XY:
AC XY:
8603
AN XY:
724606
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: 0.0164 AC: 2497AN: 152332Hom.: 63 Cov.: 33 AF XY: 0.0185 AC XY: 1376AN XY: 74484
GnomAD4 genome
?
AF:
AC:
2497
AN:
152332
Hom.:
Cov.:
33
AF XY:
AC XY:
1376
AN XY:
74484
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:
185
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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