chr4-13588756-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_148894.3(BOD1L1):c.8246T>C(p.Ile2749Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00129 in 1,605,530 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_148894.3 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 | UniProt |
---|---|---|---|---|---|---|---|
BOD1L1 | NM_148894.3 | c.8246T>C | p.Ile2749Thr | missense_variant | 15/26 | ENST00000040738.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BOD1L1 | ENST00000040738.10 | c.8246T>C | p.Ile2749Thr | missense_variant | 15/26 | 1 | NM_148894.3 | P2 | |
BOD1L1 | ENST00000507943.2 | c.8246T>C | p.Ile2749Thr | missense_variant | 15/27 | 3 | A2 | ||
BOD1L1 | ENST00000511119.1 | n.1696T>C | non_coding_transcript_exon_variant | 3/7 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00107 AC: 163AN: 152204Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00111 AC: 270AN: 243450Hom.: 3 AF XY: 0.00122 AC XY: 161AN XY: 131478
GnomAD4 exome AF: 0.00131 AC: 1903AN: 1453208Hom.: 10 Cov.: 29 AF XY: 0.00141 AC XY: 1020AN XY: 722442
GnomAD4 genome ? AF: 0.00107 AC: 163AN: 152322Hom.: 1 Cov.: 33 AF XY: 0.00113 AC XY: 84AN XY: 74498
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | BOD1L1: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at