rs78780803
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001378213.1(BCL9L):āc.1627A>Gā(p.Ser543Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0134 in 1,613,902 control chromosomes in the GnomAD database, including 467 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_001378213.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCL9L | NM_001378213.1 | c.1627A>G | p.Ser543Gly | missense_variant | 8/10 | ENST00000683865.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCL9L | ENST00000683865.1 | c.1627A>G | p.Ser543Gly | missense_variant | 8/10 | NM_001378213.1 | P4 | ||
BCL9L | ENST00000334801.7 | c.1627A>G | p.Ser543Gly | missense_variant | 6/8 | 1 | P4 | ||
BCL9L | ENST00000526143.2 | c.1516A>G | p.Ser506Gly | missense_variant | 6/8 | 5 | A1 | ||
BCL9L | ENST00000530293.1 | n.41-1355A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0224 AC: 3403AN: 151966Hom.: 86 Cov.: 32
GnomAD3 exomes AF: 0.0218 AC: 5470AN: 251150Hom.: 218 AF XY: 0.0208 AC XY: 2823AN XY: 135780
GnomAD4 exome AF: 0.0125 AC: 18281AN: 1461816Hom.: 381 Cov.: 36 AF XY: 0.0126 AC XY: 9134AN XY: 727206
GnomAD4 genome ? AF: 0.0224 AC: 3413AN: 152086Hom.: 86 Cov.: 32 AF XY: 0.0242 AC XY: 1797AN XY: 74348
ClinVar
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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at