4-76271764-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.866C>T(p.Pro289Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000271 in 1,550,978 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_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.866C>T | p.Pro289Leu | missense_variant | 5/8 | ENST00000424749.7 | |
FAM47E-STBD1 | NM_001242939.2 | c.866C>T | p.Pro289Leu | missense_variant | 5/7 | ||
FAM47E | NM_001242936.1 | c.572C>T | p.Pro191Leu | missense_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM47E | ENST00000424749.7 | c.866C>T | p.Pro289Leu | missense_variant | 5/8 | 5 | NM_001136570.3 | P1 | |
ENST00000670253.1 | n.278-9512G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152114Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000192 AC: 3AN: 155924Hom.: 0 AF XY: 0.0000242 AC XY: 2AN XY: 82616
GnomAD4 exome AF: 0.0000279 AC: 39AN: 1398864Hom.: 0 Cov.: 32 AF XY: 0.0000362 AC XY: 25AN XY: 689952
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152114Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 13, 2021 | The c.866C>T (p.P289L) alteration is located in exon 5 (coding exon 5) of the FAM47E gene. This alteration results from a C to T substitution at nucleotide position 866, causing the proline (P) at amino acid position 289 to be replaced by a leucine (L). 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