1-206909788-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005449.5(FCMR):c.922C>A(p.Pro308Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000433 in 1,448,864 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005449.5 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 |
---|---|---|---|---|---|---|---|
FCMR | NM_005449.5 | c.922C>A | p.Pro308Thr | missense_variant | 6/8 | ENST00000367091.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FCMR | ENST00000367091.8 | c.922C>A | p.Pro308Thr | missense_variant | 6/8 | 1 | NM_005449.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000302 AC: 46AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000273 AC: 13AN: 47552Hom.: 0 AF XY: 0.000399 AC XY: 11AN XY: 27586
GnomAD4 exome AF: 0.000449 AC: 582AN: 1296664Hom.: 0 Cov.: 31 AF XY: 0.000443 AC XY: 282AN XY: 637058
GnomAD4 genome AF: 0.000302 AC: 46AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 22, 2023 | The c.922C>A (p.P308T) alteration is located in exon 6 (coding exon 6) of the FCMR gene. This alteration results from a C to A substitution at nucleotide position 922, causing the proline (P) at amino acid position 308 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