chr8-72051023-T-C

Variant names:

• chr8-72051023-T-C
• rs1025928
• NM_007332.3:c.1812-152A>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.1812-152A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.619 in 619,080 control chromosomes in the GnomAD database, including 120,348 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 0.63 (30405 hom., cov: 32)
  • Exomes 𝑓: 0.62 (89943 hom.)
• Consequence: TRPA1 NM_007332.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.729
• Publications: 8 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.73 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.1812-152A>G		intron	N/A	NP_015628.2
	MSC-AS1	NR_033651.1		n.434-1516T>C		intron	N/A
	MSC-AS1	NR_033652.1		n.1029-1516T>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.1812-152A>G		intron	N/A	ENSP00000262209.4
	MSC-AS1	ENST00000457356.9	TSL:1	n.511-1516T>C		intron	N/A
	TRPA1	ENST00000523582.5	TSL:5	c.1368-152A>G		intron	N/A	ENSP00000428151.1

Frequencies

GnomAD3 genomes AF: 0.629 AC: 95610 AN: 151922 Hom.: 30361 Cov.: 32

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.639

GnomAD4 exome AF: 0.616 AC: 287796 AN: 467038 Hom.: 89943 AF XY: 0.617 AC XY: 154290 AN XY: 249926

African (AFR) AF: 0.650 AC: 8296 AN: 12766

American (AMR) AF: 0.782 AC: 17474 AN: 22344

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 9433 AN: 14438

East Asian (EAS) AF: 0.669 AC: 20098 AN: 30048

South Asian (SAS) AF: 0.666 AC: 31563 AN: 47410

European-Finnish (FIN) AF: 0.573 AC: 16648 AN: 29046

Middle Eastern (MID) AF: 0.627 AC: 1494 AN: 2382

European-Non Finnish (NFE) AF: 0.589 AC: 166382 AN: 282414

Other (OTH) AF: 0.626 AC: 16408 AN: 26190

GnomAD4 genome AF: 0.629 AC: 95704 AN: 152042 Hom.: 30405 Cov.: 32 AF XY: 0.632 AC XY: 46944 AN XY: 74308

African (AFR) AF: 0.660 AC: 27353 AN: 41474

American (AMR) AF: 0.741 AC: 11328 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2255 AN: 3470

East Asian (EAS) AF: 0.692 AC: 3570 AN: 5156

South Asian (SAS) AF: 0.674 AC: 3252 AN: 4828

European-Finnish (FIN) AF: 0.552 AC: 5829 AN: 10560

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.590 AC: 40074 AN: 67958

Other (OTH) AF: 0.636 AC: 1344 AN: 2112

Alfa AF: 0.603 Hom.: 106977

Bravo AF: 0.645

Asia WGS AF: 0.697 AC: 2426 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.28
DANN	Benign	0.47
PhyloP100		-0.73
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: rs1025928; hg19: chr8-72963258;