rs374896622
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001039933.3(CD79B):c.68-6A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000316 in 1,613,620 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001039933.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CD79B | NM_000626.4 | c.68-9A>G | intron_variant | ENST00000006750.8 | NP_000617.1 | |||
CD79B | NM_001039933.3 | c.68-6A>G | splice_region_variant, intron_variant | NP_001035022.1 | ||||
CD79B | NM_001329050.2 | c.68-6A>G | splice_region_variant, intron_variant | NP_001315979.1 | ||||
CD79B | NM_021602.4 | c.68-9A>G | intron_variant | NP_067613.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CD79B | ENST00000006750.8 | c.68-9A>G | intron_variant | 1 | NM_000626.4 | ENSP00000006750.4 | ||||
ENSG00000285947 | ENST00000647774.1 | c.-11A>G | upstream_gene_variant | ENSP00000497443.1 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152098Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000718 AC: 18AN: 250680Hom.: 0 AF XY: 0.0000737 AC XY: 10AN XY: 135752
GnomAD4 exome AF: 0.000341 AC: 498AN: 1461522Hom.: 0 Cov.: 31 AF XY: 0.000341 AC XY: 248AN XY: 727088
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152098Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74308
ClinVar
Submissions by phenotype
Agammaglobulinemia 6, autosomal recessive Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 30, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at