chr4-76256417-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001136570.3(FAM47E):c.314C>T(p.Ser105Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000193 in 1,552,286 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
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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 |
---|---|---|---|---|---|---|---|
FAM47E | NM_001136570.3 | c.314C>T | p.Ser105Leu | missense_variant | 2/8 | ENST00000424749.7 | |
FAM47E-STBD1 | NM_001242939.2 | c.314C>T | p.Ser105Leu | missense_variant | 2/7 | ||
FAM47E | NM_001242936.1 | c.82-7287C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM47E | ENST00000424749.7 | c.314C>T | p.Ser105Leu | missense_variant | 2/8 | 5 | NM_001136570.3 | P1 | |
ENST00000670253.1 | n.554+518G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000902 AC: 14AN: 155216Hom.: 0 AF XY: 0.0000972 AC XY: 8AN XY: 82312
GnomAD4 exome AF: 0.0000164 AC: 23AN: 1400108Hom.: 0 Cov.: 31 AF XY: 0.0000203 AC XY: 14AN XY: 690616
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 14, 2023 | The c.314C>T (p.S105L) alteration is located in exon 2 (coding exon 2) of the FAM47E gene. This alteration results from a C to T substitution at nucleotide position 314, causing the serine (S) at amino acid position 105 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