19-9251407-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001079935.2(OR7E24):c.364T>C(p.Phe122Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000121 in 1,614,156 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001079935.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR7E24 | NM_001079935.2 | c.364T>C | p.Phe122Leu | missense_variant | 1/1 | ENST00000456448.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR7E24 | ENST00000456448.3 | c.364T>C | p.Phe122Leu | missense_variant | 1/1 | NM_001079935.2 | P2 | ||
OR7E24 | ENST00000641946.1 | c.352T>C | p.Phe118Leu | missense_variant | 2/2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000592 AC: 90AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000136 AC: 34AN: 250426Hom.: 1 AF XY: 0.000162 AC XY: 22AN XY: 135782
GnomAD4 exome AF: 0.0000705 AC: 103AN: 1461888Hom.: 2 Cov.: 35 AF XY: 0.0000688 AC XY: 50AN XY: 727244
GnomAD4 genome ? AF: 0.000611 AC: 93AN: 152268Hom.: 0 Cov.: 32 AF XY: 0.000672 AC XY: 50AN XY: 74452
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 16, 2022 | The c.364T>C (p.F122L) alteration is located in exon 1 (coding exon 1) of the OR7E24 gene. This alteration results from a T to C substitution at nucleotide position 364, causing the phenylalanine (F) at amino acid position 122 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