chr5-108872211-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_005246.4(FER):c.922A>G(p.Met308Val) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00011 in 1,600,916 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/23 in silico tools predict a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005246.4 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
FER | NM_005246.4 | c.922A>G | p.Met308Val | missense_variant, splice_region_variant | 8/20 | ENST00000281092.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FER | ENST00000281092.9 | c.922A>G | p.Met308Val | missense_variant, splice_region_variant | 8/20 | 1 | NM_005246.4 | P1 | |
FER | ENST00000504143.6 | c.*393A>G | splice_region_variant, 3_prime_UTR_variant, NMD_transcript_variant | 6/18 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152104Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000159 AC: 38AN: 239512Hom.: 0 AF XY: 0.000192 AC XY: 25AN XY: 130062
GnomAD4 exome AF: 0.000112 AC: 162AN: 1448812Hom.: 0 Cov.: 29 AF XY: 0.000114 AC XY: 82AN XY: 720900
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152104Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74302
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 31, 2023 | The c.922A>G (p.M308V) alteration is located in exon 8 (coding exon 6) of the FER gene. This alteration results from a A to G substitution at nucleotide position 922, causing the methionine (M) at amino acid position 308 to be replaced by a valine (V). 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