chr15-29136407-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015307.2(ENTREP2):c.886C>G(p.Pro296Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000548 in 1,533,930 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P296T) has been classified as Uncertain significance.
Frequency
Consequence
NM_015307.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENTREP2 | NM_015307.2 | c.886C>G | p.Pro296Ala | missense_variant | 7/11 | ENST00000261275.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENTREP2 | ENST00000261275.5 | c.886C>G | p.Pro296Ala | missense_variant | 7/11 | 5 | NM_015307.2 | P1 | |
ENTREP2 | ENST00000560021.1 | n.622C>G | non_coding_transcript_exon_variant | 4/8 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 151928Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000786 AC: 11AN: 139938Hom.: 0 AF XY: 0.0000936 AC XY: 7AN XY: 74780
GnomAD4 exome AF: 0.0000485 AC: 67AN: 1381884Hom.: 0 Cov.: 34 AF XY: 0.0000558 AC XY: 38AN XY: 681188
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152046Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 06, 2023 | The c.886C>G (p.P296A) alteration is located in exon 7 (coding exon 7) of the FAM189A1 gene. This alteration results from a C to G substitution at nucleotide position 886, causing the proline (P) at amino acid position 296 to be replaced by an alanine (A). 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