rs116625909
Positions:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_000626.4(CD79B):c.312C>T(p.Leu104=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00145 in 1,614,228 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0079 ( 15 hom., cov: 33)
Exomes 𝑓: 0.00078 ( 17 hom. )
Consequence
CD79B
NM_000626.4 synonymous
NM_000626.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.152
Genes affected
CD79B (HGNC:1699): (CD79b molecule) The B lymphocyte antigen receptor is a multimeric complex that includes the antigen-specific component, surface immunoglobulin (Ig). Surface Ig non-covalently associates with two other proteins, Ig-alpha and Ig-beta, which are necessary for expression and function of the B-cell antigen receptor. This gene encodes the Ig-beta protein of the B-cell antigen component. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
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=-0.77).
BP6
?
Variant 17-63930192-G-A is Benign according to our data. Variant chr17-63930192-G-A is described in ClinVar as [Benign]. Clinvar id is 471350.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.152 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00788 (1201/152346) while in subpopulation AFR AF= 0.027 (1124/41580). AF 95% confidence interval is 0.0257. There are 15 homozygotes in gnomad4. There are 571 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 15 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD79B | NM_000626.4 | c.312C>T | p.Leu104= | synonymous_variant | 3/6 | ENST00000006750.8 | |
CD79B | NM_001039933.3 | c.315C>T | p.Leu105= | synonymous_variant | 3/6 | ||
CD79B | NM_001329050.2 | c.122-304C>T | intron_variant | ||||
CD79B | NM_021602.4 | c.119-304C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD79B | ENST00000006750.8 | c.312C>T | p.Leu104= | synonymous_variant | 3/6 | 1 | NM_000626.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00788 AC: 1200AN: 152228Hom.: 15 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
1200
AN:
152228
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: 0.00184 AC: 462AN: 251412Hom.: 12 AF XY: 0.00132 AC XY: 179AN XY: 135884
GnomAD3 exomes
AF:
AC:
462
AN:
251412
Hom.:
AF XY:
AC XY:
179
AN XY:
135884
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: 0.000780 AC: 1140AN: 1461882Hom.: 17 Cov.: 34 AF XY: 0.000644 AC XY: 468AN XY: 727240
GnomAD4 exome
AF:
AC:
1140
AN:
1461882
Hom.:
Cov.:
34
AF XY:
AC XY:
468
AN XY:
727240
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: 0.00788 AC: 1201AN: 152346Hom.: 15 Cov.: 33 AF XY: 0.00766 AC XY: 571AN XY: 74496
GnomAD4 genome
?
AF:
AC:
1201
AN:
152346
Hom.:
Cov.:
33
AF XY:
AC XY:
571
AN XY:
74496
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:
4
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Agammaglobulinemia 6, autosomal recessive Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
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