chr8-72029895-A-G
Position:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_007332.3(TRPA1):c.2937+6T>C variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00445 in 1,613,732 control chromosomes in the GnomAD database, including 38 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0035 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0045 ( 36 hom. )
Consequence
TRPA1
NM_007332.3 splice_donor_region, intron
NM_007332.3 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.1393
2
Clinical Significance
Conservation
PhyloP100: 2.37
Genes affected
TRPA1 (HGNC:497): (transient receptor potential cation channel subfamily A member 1) The structure of the protein encoded by this gene is highly related to both the protein ankyrin and transmembrane proteins. The specific function of this protein has not yet been determined; however, studies indicate the function may involve a role in signal transduction and growth control. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
Variant 8-72029895-A-G is Benign according to our data. Variant chr8-72029895-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 788822.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High AC in GnomAd4 at 535 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRPA1 | NM_007332.3 | c.2937+6T>C | splice_donor_region_variant, intron_variant | ENST00000262209.5 | |||
MSC-AS1 | NR_033652.1 | n.1029-22644A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRPA1 | ENST00000262209.5 | c.2937+6T>C | splice_donor_region_variant, intron_variant | 1 | NM_007332.3 | P1 | |||
MSC-AS1 | ENST00000518916.5 | n.392-22644A>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00352 AC: 535AN: 152198Hom.: 2 Cov.: 32
GnomAD3 genomes
AF:
AC:
535
AN:
152198
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00436 AC: 1095AN: 251014Hom.: 4 AF XY: 0.00456 AC XY: 618AN XY: 135646
GnomAD3 exomes
AF:
AC:
1095
AN:
251014
Hom.:
AF XY:
AC XY:
618
AN XY:
135646
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00454 AC: 6639AN: 1461416Hom.: 36 Cov.: 30 AF XY: 0.00455 AC XY: 3311AN XY: 727030
GnomAD4 exome
AF:
AC:
6639
AN:
1461416
Hom.:
Cov.:
30
AF XY:
AC XY:
3311
AN XY:
727030
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00351 AC: 535AN: 152316Hom.: 2 Cov.: 32 AF XY: 0.00365 AC XY: 272AN XY: 74484
GnomAD4 genome
AF:
AC:
535
AN:
152316
Hom.:
Cov.:
32
AF XY:
AC XY:
272
AN XY:
74484
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | TRPA1: BP4, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at