rs561845

Positions:

• chr11-118688118-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000531328.2(TREHP1):​n.426T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 1,023,758 control chromosomes in the GnomAD database, including 82,781 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 0.32 (8112 hom., cov: 32)
  • Exomes 𝑓: 0.38 (74669 hom.)
• Consequence: TREHP1 ENST00000531328.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.94

Genes affected

TREHP1 (HGNC:51907): (trehalase pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TREHP1	ENST00000531328.2	n.426T>C		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48372 AN: 151974 Hom.: 8098 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.334

GnomAD4 exome AF: 0.381 AC: 331804 AN: 871668 Hom.: 74669 Cov.: 13 AF XY: 0.384 AC XY: 162258 AN XY: 423010

Gnomad4 AFR exome AF: 0.313

Gnomad4 AMR exome AF: 0.722

Gnomad4 ASJ exome AF: 0.529

Gnomad4 EAS exome AF: 0.687

Gnomad4 SAS exome AF: 0.283

Gnomad4 FIN exome AF: 0.432

Gnomad4 NFE exome AF: 0.363

Gnomad4 OTH exome AF: 0.389

GnomAD4 genome AF: 0.318 AC: 48404 AN: 152090 Hom.: 8112 Cov.: 32 AF XY: 0.318 AC XY: 23678 AN XY: 74346

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.363

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.333

Alfa AF: 0.328 Hom.: 1040

Bravo AF: 0.333

Asia WGS AF: 0.270 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	14
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs561845; hg19: chr11-118558827;