11-124310573-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001002917.2(OR8D1):c.194G>T(p.Ser65Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000366 in 1,613,754 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_001002917.2 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 |
---|---|---|---|---|---|---|---|
OR8D1 | NM_001002917.2 | c.194G>T | p.Ser65Ile | missense_variant | 3/3 | ENST00000641015.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR8D1 | ENST00000641015.1 | c.194G>T | p.Ser65Ile | missense_variant | 3/3 | NM_001002917.2 | P1 | ||
OR8D1 | ENST00000357821.2 | c.194G>T | p.Ser65Ile | missense_variant | 1/1 | P1 | |||
OR8D1 | ENST00000641897.1 | c.194G>T | p.Ser65Ile | missense_variant | 4/4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152078Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000207 AC: 52AN: 250726Hom.: 0 AF XY: 0.000185 AC XY: 25AN XY: 135486
GnomAD4 exome AF: 0.0000390 AC: 57AN: 1461676Hom.: 0 Cov.: 33 AF XY: 0.0000385 AC XY: 28AN XY: 727128
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152078Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74262
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | The c.194G>T (p.S65I) alteration is located in exon 1 (coding exon 1) of the OR8D1 gene. This alteration results from a G to T substitution at nucleotide position 194, causing the serine (S) at amino acid position 65 to be replaced by an isoleucine (I). 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