chr11-118898594-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001378213.1(BCL9L):c.4321G>A(p.Val1441Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00105 in 1,611,814 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
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.4321G>A | p.Val1441Met | missense_variant | 10/10 | ENST00000683865.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCL9L | ENST00000683865.1 | c.4321G>A | p.Val1441Met | missense_variant | 10/10 | NM_001378213.1 | P4 | ||
BCL9L | ENST00000334801.7 | c.4321G>A | p.Val1441Met | missense_variant | 8/8 | 1 | P4 | ||
BCL9L | ENST00000526143.2 | c.4210G>A | p.Val1404Met | missense_variant | 8/8 | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00513 AC: 781AN: 152198Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00128 AC: 313AN: 243620Hom.: 4 AF XY: 0.00111 AC XY: 148AN XY: 133232
GnomAD4 exome AF: 0.000626 AC: 914AN: 1459498Hom.: 4 Cov.: 35 AF XY: 0.000561 AC XY: 407AN XY: 725992
GnomAD4 genome ? AF: 0.00513 AC: 782AN: 152316Hom.: 6 Cov.: 32 AF XY: 0.00499 AC XY: 372AN XY: 74476
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at