rs12541758

Variant names:

• chr8-72230147-C-T
• rs12541758
• ENST00000503430.1:n.1424G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000503430.1(TRPA2P):​n.1424G>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.417 in 1,612,494 control chromosomes in the GnomAD database, including 144,815 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 0.34 (10557 hom., cov: 31)
  • Exomes 𝑓: 0.42 (134258 hom.)
• Consequence: TRPA2P ENST00000503430.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.88
• Publications: 8 publications found

Genes affected

TRPA2P (HGNC:57045):

ENSG00000304447 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TRPA2P	NR_033867.2	n.1165G>A		non_coding_transcript_exon_variant	Exon 9 of 20

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TRPA2P	ENST00000503430.1	n.1424G>A		non_coding_transcript_exon_variant	Exon 12 of 25	6
ENSG00000304447	ENST00000803509.1	n.1230G>A		non_coding_transcript_exon_variant	Exon 10 of 13
ENSG00000304447	ENST00000803510.1	n.1297G>A		non_coding_transcript_exon_variant	Exon 8 of 8

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52318 AN: 151916 Hom.: 10556 Cov.: 31

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.348

GnomAD4 exome AF: 0.425 AC: 620621 AN: 1460458 Hom.: 134258 Cov.: 34 AF XY: 0.425 AC XY: 309113 AN XY: 726600

African (AFR) AF: 0.109 AC: 3638 AN: 33452

American (AMR) AF: 0.401 AC: 17916 AN: 44708

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 12624 AN: 26126

East Asian (EAS) AF: 0.402 AC: 15948 AN: 39682

South Asian (SAS) AF: 0.390 AC: 33623 AN: 86238

European-Finnish (FIN) AF: 0.480 AC: 25621 AN: 53412

Middle Eastern (MID) AF: 0.430 AC: 2474 AN: 5760

European-Non Finnish (NFE) AF: 0.436 AC: 484342 AN: 1110732

Other (OTH) AF: 0.405 AC: 24435 AN: 60348

GnomAD4 genome AF: 0.344 AC: 52331 AN: 152036 Hom.: 10557 Cov.: 31 AF XY: 0.347 AC XY: 25779 AN XY: 74316

African (AFR) AF: 0.117 AC: 4872 AN: 41496

American (AMR) AF: 0.389 AC: 5941 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1638 AN: 3468

East Asian (EAS) AF: 0.379 AC: 1948 AN: 5138

South Asian (SAS) AF: 0.395 AC: 1902 AN: 4814

European-Finnish (FIN) AF: 0.484 AC: 5108 AN: 10558

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.437 AC: 29725 AN: 67976

Other (OTH) AF: 0.347 AC: 732 AN: 2108

Alfa AF: 0.343 Hom.: 1545

Bravo AF: 0.325

Asia WGS AF: 0.372 AC: 1291 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	17
DANN	Benign	0.61
PhyloP100		6.9

Splicing

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

Other links and lift over

dbSNP: rs12541758; hg19: chr8-73142382;