12-122054976-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000538010.5(BCL7A):āc.611T>Cā(p.Ile204Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000359 in 1,613,606 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
ENST00000538010.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCL7A | NM_001024808.3 | c.561+50T>C | intron_variant | ENST00000261822.5 | |||
BCL7A | NM_020993.5 | c.611T>C | p.Ile204Thr | missense_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCL7A | ENST00000538010.5 | c.611T>C | p.Ile204Thr | missense_variant | 5/6 | 1 | |||
BCL7A | ENST00000261822.5 | c.561+50T>C | intron_variant | 1 | NM_001024808.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152036Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000439 AC: 11AN: 250798Hom.: 0 AF XY: 0.0000738 AC XY: 10AN XY: 135586
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461570Hom.: 0 Cov.: 32 AF XY: 0.0000358 AC XY: 26AN XY: 727114
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152036Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74266
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 03, 2022 | The c.611T>C (p.I204T) alteration is located in exon 5 (coding exon 5) of the BCL7A gene. This alteration results from a T to C substitution at nucleotide position 611, causing the isoleucine (I) at amino acid position 204 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at