chr17-3577139-G-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_080704.4(TRPV1):c.1767C>G(p.Phe589Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00155 in 1,586,946 control chromosomes in the GnomAD database, including 4 homozygotes. 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 Likely benign (★).
Frequency
Consequence
NM_080704.4 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 |
---|---|---|---|---|---|---|---|
TRPV1 | NM_080704.4 | c.1767C>G | p.Phe589Leu | missense_variant | 13/17 | ENST00000572705.2 | |
TRPV1 | NM_018727.5 | c.1767C>G | p.Phe589Leu | missense_variant | 12/16 | ||
TRPV1 | NM_080705.4 | c.1767C>G | p.Phe589Leu | missense_variant | 12/16 | ||
TRPV1 | NM_080706.3 | c.1767C>G | p.Phe589Leu | missense_variant | 11/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPV1 | ENST00000572705.2 | c.1767C>G | p.Phe589Leu | missense_variant | 13/17 | 1 | NM_080704.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000940 AC: 143AN: 152124Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000927 AC: 193AN: 208094Hom.: 1 AF XY: 0.000850 AC XY: 95AN XY: 111746
GnomAD4 exome AF: 0.00162 AC: 2320AN: 1434704Hom.: 3 Cov.: 33 AF XY: 0.00154 AC XY: 1093AN XY: 710978
GnomAD4 genome ? AF: 0.000939 AC: 143AN: 152242Hom.: 1 Cov.: 32 AF XY: 0.000941 AC XY: 70AN XY: 74424
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 19, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at