chr5-108883500-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_005246.4(FER):c.1028C>T(p.Thr343Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,602,428 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005246.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FER | NM_005246.4 | c.1028C>T | p.Thr343Ile | missense_variant | 9/20 | ENST00000281092.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FER | ENST00000281092.9 | c.1028C>T | p.Thr343Ile | missense_variant | 9/20 | 1 | NM_005246.4 | P1 | |
FER | ENST00000504143.6 | c.*499C>T | 3_prime_UTR_variant, NMD_transcript_variant | 7/18 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151902Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000145 AC: 21AN: 1450526Hom.: 0 Cov.: 30 AF XY: 0.0000166 AC XY: 12AN XY: 721538
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151902Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74180
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 10, 2022 | The c.1028C>T (p.T343I) alteration is located in exon 9 (coding exon 7) of the FER gene. This alteration results from a C to T substitution at nucleotide position 1028, causing the threonine (T) at amino acid position 343 to be replaced by an isoleucine (I). 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