15-29123568-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015307.2(ENTREP2):āc.1391C>Gā(p.Pro464Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 1,551,634 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_015307.2 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 |
---|---|---|---|---|---|---|---|
ENTREP2 | NM_015307.2 | c.1391C>G | p.Pro464Arg | missense_variant | 11/11 | ENST00000261275.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENTREP2 | ENST00000261275.5 | c.1391C>G | p.Pro464Arg | missense_variant | 11/11 | 5 | NM_015307.2 | P1 | |
ENTREP2 | ENST00000560021.1 | n.1127C>G | non_coding_transcript_exon_variant | 8/8 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152212Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000643 AC: 1AN: 155498Hom.: 0 AF XY: 0.0000121 AC XY: 1AN XY: 82474
GnomAD4 exome AF: 0.0000329 AC: 46AN: 1399422Hom.: 0 Cov.: 35 AF XY: 0.0000304 AC XY: 21AN XY: 690224
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152212Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 27, 2022 | The c.1391C>G (p.P464R) alteration is located in exon 11 (coding exon 11) of the FAM189A1 gene. This alteration results from a C to G substitution at nucleotide position 1391, causing the proline (P) at amino acid position 464 to be replaced by an arginine (R). 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