chr17-3580491-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_080704.4(TRPV1):c.1513A>G(p.Thr505Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00403 in 1,613,960 control chromosomes in the GnomAD database, including 28 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
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.1513A>G | p.Thr505Ala | missense_variant | 11/17 | ENST00000572705.2 | |
TRPV1 | NM_018727.5 | c.1513A>G | p.Thr505Ala | missense_variant | 10/16 | ||
TRPV1 | NM_080705.4 | c.1513A>G | p.Thr505Ala | missense_variant | 10/16 | ||
TRPV1 | NM_080706.3 | c.1513A>G | p.Thr505Ala | missense_variant | 9/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPV1 | ENST00000572705.2 | c.1513A>G | p.Thr505Ala | missense_variant | 11/17 | 1 | NM_080704.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00296 AC: 450AN: 152136Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00384 AC: 958AN: 249262Hom.: 6 AF XY: 0.00439 AC XY: 593AN XY: 135226
GnomAD4 exome AF: 0.00414 AC: 6055AN: 1461706Hom.: 26 Cov.: 31 AF XY: 0.00430 AC XY: 3126AN XY: 727138
GnomAD4 genome ? AF: 0.00295 AC: 449AN: 152254Hom.: 2 Cov.: 32 AF XY: 0.00281 AC XY: 209AN XY: 74448
ClinVar
Submissions by phenotype
not provided Benign:1
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