chr1-93530747-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001164473.3(FNBP1L):c.511-8G>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00693 in 1,594,810 control chromosomes in the GnomAD database, including 62 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001164473.3 splice_region, splice_polypyrimidine_tract, intron
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 |
---|---|---|---|---|---|---|---|
FNBP1L | NM_001164473.3 | c.511-8G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000271234.13 | |||
FNBP1L | NM_001024948.3 | c.511-8G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
FNBP1L | NM_017737.5 | c.511-8G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FNBP1L | ENST00000271234.13 | c.511-8G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | NM_001164473.3 | ||||
FNBP1L | ENST00000260506.12 | c.511-8G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | P4 | ||||
FNBP1L | ENST00000370253.6 | c.511-8G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | A1 | ||||
FNBP1L | ENST00000424449.2 | c.48-8G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00475 AC: 722AN: 152126Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00517 AC: 1160AN: 224190Hom.: 8 AF XY: 0.00582 AC XY: 703AN XY: 120706
GnomAD4 exome AF: 0.00716 AC: 10331AN: 1442566Hom.: 59 Cov.: 30 AF XY: 0.00734 AC XY: 5250AN XY: 715720
GnomAD4 genome ? AF: 0.00474 AC: 722AN: 152244Hom.: 3 Cov.: 32 AF XY: 0.00422 AC XY: 314AN XY: 74452
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jun 23, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at