chr3-187729200-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001706.5(BCL6):c.1205G>A(p.Arg402His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000206 in 1,592,922 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001706.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BCL6 | NM_001706.5 | c.1205G>A | p.Arg402His | missense_variant | 5/10 | ENST00000406870.7 | NP_001697.2 | |
LOC100131635 | NR_034062.1 | n.294-3171C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BCL6 | ENST00000406870.7 | c.1205G>A | p.Arg402His | missense_variant | 5/10 | 1 | NM_001706.5 | ENSP00000384371 | P1 | |
ENST00000449623.5 | n.347-4324C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00106 AC: 160AN: 151280Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000322 AC: 80AN: 248276Hom.: 1 AF XY: 0.000216 AC XY: 29AN XY: 134150
GnomAD4 exome AF: 0.000117 AC: 168AN: 1441522Hom.: 1 Cov.: 31 AF XY: 0.000107 AC XY: 77AN XY: 716496
GnomAD4 genome AF: 0.00106 AC: 160AN: 151400Hom.: 0 Cov.: 32 AF XY: 0.000973 AC XY: 72AN XY: 74024
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 19, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at