7-72926937-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001387691.1(POM121):c.996C>A(p.Phe332Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,942 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001387691.1 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POM121 | NM_001387691.1 | c.996C>A | p.Phe332Leu | missense_variant | Exon 3 of 13 | ENST00000434423.5 | NP_001374620.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
POM121 | ENST00000434423.5 | c.996C>A | p.Phe332Leu | missense_variant | Exon 3 of 13 | 5 | NM_001387691.1 | ENSP00000405562.2 | ||
POM121 | ENST00000395270.5 | c.201C>A | p.Phe67Leu | missense_variant | Exon 6 of 16 | 1 | ENSP00000378687.1 | |||
POM121 | ENST00000627934.3 | c.201C>A | p.Phe67Leu | missense_variant | Exon 5 of 15 | 5 | ENSP00000486504.1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251180Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135744
GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461668Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9AN XY: 727144
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.201C>A (p.F67L) alteration is located in exon 5 (coding exon 2) of the POM121 gene. This alteration results from a C to A substitution at nucleotide position 201, causing the phenylalanine (F) at amino acid position 67 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