8-72036324-T-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_007332.3(TRPA1):āc.2519A>Cā(p.Tyr840Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,613,966 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_007332.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRPA1 | NM_007332.3 | c.2519A>C | p.Tyr840Ser | missense_variant | 21/27 | ENST00000262209.5 | |
MSC-AS1 | NR_033652.1 | n.1029-16215T>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPA1 | ENST00000262209.5 | c.2519A>C | p.Tyr840Ser | missense_variant | 21/27 | 1 | NM_007332.3 | P1 | |
MSC-AS1 | ENST00000518916.5 | n.392-16215T>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251060Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135704
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461786Hom.: 0 Cov.: 31 AF XY: 0.0000385 AC XY: 28AN XY: 727186
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 04, 2023 | The c.2519A>C (p.Y840S) alteration is located in exon 21 (coding exon 21) of the TRPA1 gene. This alteration results from a A to C substitution at nucleotide position 2519, causing the tyrosine (Y) at amino acid position 840 to be replaced by a serine (S). 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