chr4-80266930-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_004464.4(FGF5):c.106G>A(p.Ala36Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000675 in 1,614,172 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004464.4 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 |
---|---|---|---|---|---|---|---|
FGF5 | NM_004464.4 | c.106G>A | p.Ala36Thr | missense_variant | 1/3 | ENST00000312465.12 | |
FGF5 | NM_033143.2 | c.106G>A | p.Ala36Thr | missense_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FGF5 | ENST00000312465.12 | c.106G>A | p.Ala36Thr | missense_variant | 1/3 | 1 | NM_004464.4 | P1 | |
FGF5 | ENST00000456523.3 | c.106G>A | p.Ala36Thr | missense_variant | 1/2 | 1 | |||
FGF5 | ENST00000380628.3 | n.106G>A | non_coding_transcript_exon_variant | 1/2 | 1 | ||||
FGF5 | ENST00000507780.1 | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152244Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000127 AC: 32AN: 251054Hom.: 1 AF XY: 0.000169 AC XY: 23AN XY: 135762
GnomAD4 exome AF: 0.0000711 AC: 104AN: 1461810Hom.: 2 Cov.: 31 AF XY: 0.000105 AC XY: 76AN XY: 727208
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152362Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74506
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 16, 2022 | The c.106G>A (p.A36T) alteration is located in exon 1 (coding exon 1) of the FGF5 gene. This alteration results from a G to A substitution at nucleotide position 106, causing the alanine (A) at amino acid position 36 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