1-93536368-A-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001164473.3(FNBP1L):c.1027A>C(p.Thr343Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000142 in 1,548,760 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001164473.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FNBP1L | NM_001164473.3 | c.1027A>C | p.Thr343Pro | missense_variant | 10/17 | ENST00000271234.13 | |
FNBP1L | NM_001024948.3 | c.990+1460A>C | intron_variant | ||||
FNBP1L | NM_017737.5 | c.990+1460A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FNBP1L | ENST00000271234.13 | c.1027A>C | p.Thr343Pro | missense_variant | 10/17 | 5 | NM_001164473.3 | ||
FNBP1L | ENST00000260506.12 | c.990+1460A>C | intron_variant | 1 | P4 | ||||
FNBP1L | ENST00000424449.2 | c.565A>C | p.Thr189Pro | missense_variant | 5/12 | 2 | |||
FNBP1L | ENST00000370253.6 | c.990+1460A>C | intron_variant | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151990Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000192 AC: 3AN: 156576Hom.: 0 AF XY: 0.0000121 AC XY: 1AN XY: 82736
GnomAD4 exome AF: 0.0000143 AC: 20AN: 1396770Hom.: 0 Cov.: 30 AF XY: 0.0000116 AC XY: 8AN XY: 688992
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151990Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74252
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 25, 2023 | The c.1027A>C (p.T343P) alteration is located in exon 10 (coding exon 10) of the FNBP1L gene. This alteration results from a A to C substitution at nucleotide position 1027, causing the threonine (T) at amino acid position 343 to be replaced by a proline (P). 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