11-5755696-A-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001005175.5(OR52N4):āc.956A>Gā(p.Tyr319Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00473 in 1,612,598 control chromosomes in the GnomAD database, including 42 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_001005175.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OR52N4 | NM_001005175.5 | c.956A>G | p.Tyr319Cys | missense_variant | 2/2 | ENST00000641350.2 | |
OR52N4 | XM_017017711.3 | c.956A>G | p.Tyr319Cys | missense_variant | 5/5 | ||
OR52N4 | XM_017017713.3 | c.956A>G | p.Tyr319Cys | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OR52N4 | ENST00000641350.2 | c.956A>G | p.Tyr319Cys | missense_variant | 2/2 | NM_001005175.5 | P1 | ||
TRIM5 | ENST00000412903.1 | c.-61-75458T>C | intron_variant | 1 | |||||
TRIM5 | ENST00000380027.5 | c.-440-70302T>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00437 AC: 665AN: 152218Hom.: 6 Cov.: 33
GnomAD3 exomes AF: 0.00453 AC: 1118AN: 247054Hom.: 10 AF XY: 0.00462 AC XY: 619AN XY: 133970
GnomAD4 exome AF: 0.00477 AC: 6965AN: 1460262Hom.: 36 Cov.: 36 AF XY: 0.00478 AC XY: 3469AN XY: 726322
GnomAD4 genome AF: 0.00436 AC: 664AN: 152336Hom.: 6 Cov.: 33 AF XY: 0.00513 AC XY: 382AN XY: 74486
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 23, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at