19-50476351-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001308429.2(GARIN5A):c.38C>T(p.Pro13Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000211 in 1,424,278 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001308429.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GARIN5A | NM_001308429.2 | c.38C>T | p.Pro13Leu | missense_variant | 1/5 | ENST00000600100.6 | |
GARIN5A | NM_138411.3 | c.38C>T | p.Pro13Leu | missense_variant | 1/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GARIN5A | ENST00000600100.6 | c.38C>T | p.Pro13Leu | missense_variant | 1/5 | 1 | NM_001308429.2 | A2 | |
GARIN5A | ENST00000595790.5 | c.38C>T | p.Pro13Leu | missense_variant | 1/5 | 1 | P2 | ||
EMC10 | ENST00000601780.5 | upstream_gene_variant | 1 | ||||||
GARIN5A | ENST00000599206.1 | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000211 AC: 3AN: 1424278Hom.: 0 Cov.: 32 AF XY: 0.00000142 AC XY: 1AN XY: 704554
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 22, 2023 | The c.38C>T (p.P13L) alteration is located in exon 1 (coding exon 1) of the FAM71E1 gene. This alteration results from a C to T substitution at nucleotide position 38, causing the proline (P) at amino acid position 13 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
Publications
No publications associated with this variant yet.