chr8-72230147-C-T

Position:

• chr8-72230147-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_033867.2(TRPA2P):​n.1165G>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 NR_033867.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.88

Genes affected

ENSG00000250979 (HGNC:57045):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
TRPA2P	NR_033867.2	n.1165G>A		non_coding_transcript_exon_variant	9/20

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000250979	ENST00000503430.1	n.1424G>A		non_coding_transcript_exon_variant	12/25	6

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

Gnomad4 AFR exome AF: 0.109

Gnomad4 AMR exome AF: 0.401

Gnomad4 ASJ exome AF: 0.483

Gnomad4 EAS exome AF: 0.402

Gnomad4 SAS exome AF: 0.390

Gnomad4 FIN exome AF: 0.480

Gnomad4 NFE exome AF: 0.436

Gnomad4 OTH exome AF: 0.405

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

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.379

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.347

Alfa AF: 0.350 Hom.: 1536

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12541758; hg19: chr8-73142382;