9-129900442-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_015033.3(FNBP1):c.1534G>A(p.Ala512Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000113 in 1,598,754 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A512P) has been classified as Uncertain significance.
Frequency
Consequence
NM_015033.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152236Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000128 AC: 3AN: 233824Hom.: 0 AF XY: 0.00000785 AC XY: 1AN XY: 127408
GnomAD4 exome AF: 0.00000622 AC: 9AN: 1446400Hom.: 0 Cov.: 30 AF XY: 0.00000278 AC XY: 2AN XY: 719382
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152354Hom.: 0 Cov.: 31 AF XY: 0.0000940 AC XY: 7AN XY: 74504
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1534G>A (p.A512T) alteration is located in exon 14 (coding exon 14) of the FNBP1 gene. This alteration results from a G to A substitution at nucleotide position 1534, causing the alanine (A) at amino acid position 512 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