rs6080718
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 2P and 17B. PM2BP4_StrongBP6_Very_StrongBP7BS1
The NM_001195.5(BFSP1):c.1749A>T(p.Pro583=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000227 in 1,614,080 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P583P) has been classified as Benign.
Frequency
Consequence
NM_001195.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BFSP1 | NM_001195.5 | c.1749A>T | p.Pro583= | synonymous_variant | 8/8 | ENST00000377873.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BFSP1 | ENST00000377873.8 | c.1749A>T | p.Pro583= | synonymous_variant | 8/8 | 1 | NM_001195.5 | P1 | |
BFSP1 | ENST00000377868.6 | c.1374A>T | p.Pro458= | synonymous_variant | 8/8 | 1 | |||
BFSP1 | ENST00000536626.7 | c.1332A>T | p.Pro444= | synonymous_variant | 9/9 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00134 AC: 204AN: 152078Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000410 AC: 103AN: 251436Hom.: 0 AF XY: 0.000265 AC XY: 36AN XY: 135898
GnomAD4 exome AF: 0.000111 AC: 162AN: 1461884Hom.: 0 Cov.: 87 AF XY: 0.0000825 AC XY: 60AN XY: 727244
GnomAD4 genome ? AF: 0.00134 AC: 204AN: 152196Hom.: 0 Cov.: 33 AF XY: 0.00114 AC XY: 85AN XY: 74414
ClinVar
Submissions by phenotype
Cataract 33 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 11, 2023 | - - |
BFSP1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 10, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at