19-9214614-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001005191.3(OR7D4):c.224C>G(p.Ser75Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000274 in 1,461,792 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S75T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001005191.3 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 |
---|---|---|---|---|---|---|---|
OR7D4 | NM_001005191.3 | c.224C>G | p.Ser75Cys | missense_variant | 2/2 | ENST00000641669.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR7D4 | ENST00000641669.1 | c.224C>G | p.Ser75Cys | missense_variant | 2/2 | NM_001005191.3 | P1 | ||
OR7D4 | ENST00000308682.3 | c.224C>G | p.Ser75Cys | missense_variant | 1/1 | P1 | |||
OR7D4 | ENST00000641244.1 | c.224C>G | p.Ser75Cys | missense_variant | 2/2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 152198Hom.: 0 Cov.: 31 FAILED QC
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251386Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135850
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461792Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 727208
GnomAD4 genome ? Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 152198Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2021 | The c.224C>G (p.S75C) alteration is located in exon 1 (coding exon 1) of the OR7D4 gene. This alteration results from a C to G substitution at nucleotide position 224, causing the serine (S) at amino acid position 75 to be replaced by a cysteine (C). 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