4-76268751-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001136570.3(FAM47E):c.652C>T(p.Pro218Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000193 in 1,551,382 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001136570.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM47E | NM_001136570.3 | c.652C>T | p.Pro218Ser | missense_variant | 4/8 | ENST00000424749.7 | |
FAM47E-STBD1 | NM_001242939.2 | c.652C>T | p.Pro218Ser | missense_variant | 4/7 | ||
FAM47E | NM_001242936.1 | c.313C>T | p.Pro105Ser | missense_variant | 4/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM47E | ENST00000424749.7 | c.652C>T | p.Pro218Ser | missense_variant | 4/8 | 5 | NM_001136570.3 | P1 | |
ENST00000670253.1 | n.278-6499G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000143 AC: 2AN: 1399202Hom.: 0 Cov.: 30 AF XY: 0.00000145 AC XY: 1AN XY: 690112
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 05, 2021 | The c.652C>T (p.P218S) alteration is located in exon 4 (coding exon 4) of the FAM47E gene. This alteration results from a C to T substitution at nucleotide position 652, causing the proline (P) at amino acid position 218 to be replaced by a serine (S). 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