8-72028115-G-C

Variant names:

• chr8-72028115-G-C
• rs12550748
• NM_007332.3:c.2937+1786C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007332.3(TRPA1):​c.2937+1786C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,118 control chromosomes in the GnomAD database, including 1,190 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (1190 hom., cov: 32)
• Consequence: TRPA1 NM_007332.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.435
• Publications: 2 publications found

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]

MSC-AS1 (HGNC:48724): (MSC antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007332.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPA1	NM_007332.3	MANE Select	c.2937+1786C>G		intron	N/A	NP_015628.2
	MSC-AS1	NR_033651.1		n.434-24424G>C		intron	N/A
	MSC-AS1	NR_033652.1		n.1029-24424G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TRPA1	ENST00000262209.5	TSL:1 MANE Select	c.2937+1786C>G		intron	N/A	ENSP00000262209.4
	MSC-AS1	ENST00000457356.9	TSL:1	n.511-24424G>C		intron	N/A
	TRPA1	ENST00000523582.5	TSL:5	c.2493+1786C>G		intron	N/A	ENSP00000428151.1

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16851 AN: 152000 Hom.: 1191 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.0354

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.0782

Gnomad MID AF: 0.0796

Gnomad NFE AF: 0.0788

Gnomad OTH AF: 0.117

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.111 AC: 16851 AN: 152118 Hom.: 1190 Cov.: 32 AF XY: 0.114 AC XY: 8458 AN XY: 74368

African (AFR) AF: 0.108 AC: 4484 AN: 41486

American (AMR) AF: 0.232 AC: 3547 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0354 AC: 123 AN: 3472

East Asian (EAS) AF: 0.204 AC: 1057 AN: 5174

South Asian (SAS) AF: 0.217 AC: 1047 AN: 4822

European-Finnish (FIN) AF: 0.0782 AC: 828 AN: 10584

Middle Eastern (MID) AF: 0.0788 AC: 23 AN: 292

European-Non Finnish (NFE) AF: 0.0788 AC: 5356 AN: 67988

Other (OTH) AF: 0.114 AC: 242 AN: 2114

Alfa AF: 0.0942 Hom.: 91

Bravo AF: 0.123

Asia WGS AF: 0.212 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.72
DANN	Benign	0.41
PhyloP100		-0.43
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12550748; hg19: chr8-72940350;