chr11-6002895-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001005179.4(OR56A4):c.98C>T(p.Pro33Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000719 in 1,614,060 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001005179.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR56A4 | NM_001005179.4 | c.98C>T | p.Pro33Leu | missense_variant | 3/3 | ENST00000641156.1 | |
OR56A3 | XM_047426926.1 | c.*469-825G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR56A4 | ENST00000641156.1 | c.98C>T | p.Pro33Leu | missense_variant | 3/3 | NM_001005179.4 | P1 | ||
OR56A4 | ENST00000330728.4 | c.254C>T | p.Pro85Leu | missense_variant | 1/1 | ||||
OR56A4 | ENST00000641279.1 | c.98C>T | p.Pro33Leu | missense_variant | 1/1 | P1 | |||
OR56A4 | ENST00000641835.1 | c.98C>T | p.Pro33Leu | missense_variant | 2/2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251244Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135776
GnomAD4 exome AF: 0.0000752 AC: 110AN: 1461814Hom.: 0 Cov.: 32 AF XY: 0.0000798 AC XY: 58AN XY: 727200
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74440
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 27, 2021 | The c.254C>T (p.P85L) alteration is located in exon 1 (coding exon 1) of the OR56A4 gene. This alteration results from a C to T substitution at nucleotide position 254, causing the proline (P) at amino acid position 85 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