11-6027455-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001388488.1(OR56A1):c.238G>A(p.Val80Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000508 in 1,614,106 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001388488.1 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR56A1 | NM_001388488.1 | c.238G>A | p.Val80Ile | missense_variant | 2/2 | ENST00000641900.1 | |
LOC107984303 | XR_001748102.2 | n.89+5367C>T | intron_variant, non_coding_transcript_variant | ||||
OR56A1 | NM_001001917.5 | c.238G>A | p.Val80Ile | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR56A1 | ENST00000641900.1 | c.238G>A | p.Val80Ile | missense_variant | 2/2 | NM_001388488.1 | P1 | ||
OR56A1 | ENST00000641423.1 | c.238G>A | p.Val80Ile | missense_variant | 2/2 | P1 | |||
OR56A1 | ENST00000641938.1 | c.238G>A | p.Val80Ile | missense_variant | 1/1 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152110Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000558 AC: 14AN: 251118Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135702
GnomAD4 exome AF: 0.0000451 AC: 66AN: 1461878Hom.: 0 Cov.: 33 AF XY: 0.0000495 AC XY: 36AN XY: 727236
GnomAD4 genome AF: 0.000105 AC: 16AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74426
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at