chr22-23181415-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_004327.4(BCR):c.455C>T(p.Ala152Val) variant causes a missense change. The variant allele was found at a frequency of 0.0021 in 1,575,312 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A152T) has been classified as Uncertain significance.
Frequency
Consequence
NM_004327.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCR | NM_004327.4 | c.455C>T | p.Ala152Val | missense_variant | 1/23 | ENST00000305877.13 | |
BCR | NM_021574.3 | c.455C>T | p.Ala152Val | missense_variant | 1/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCR | ENST00000305877.13 | c.455C>T | p.Ala152Val | missense_variant | 1/23 | 1 | NM_004327.4 | P1 | |
BCR | ENST00000359540.7 | c.455C>T | p.Ala152Val | missense_variant | 1/22 | 1 | |||
BCR | ENST00000479188.5 | n.129+1583C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00205 AC: 311AN: 152056Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00272 AC: 589AN: 216466Hom.: 5 AF XY: 0.00276 AC XY: 332AN XY: 120122
GnomAD4 exome AF: 0.00211 AC: 3005AN: 1423140Hom.: 15 Cov.: 31 AF XY: 0.00211 AC XY: 1483AN XY: 703880
GnomAD4 genome ? AF: 0.00204 AC: 311AN: 152172Hom.: 1 Cov.: 32 AF XY: 0.00238 AC XY: 177AN XY: 74394
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2024 | BCR: BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 23, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at