rs561845

Variant names:

• chr11-118688118-A-G
• rs561845
• ENST00000531328.2:n.426T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TREHP1		n.118688118A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TREHP1	ENST00000531328.2	n.426T>C		non_coding_transcript_exon_variant	Exon 4 of 4	6

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

African (AFR) AF: 0.313 AC: 5329 AN: 17034

American (AMR) AF: 0.722 AC: 13595 AN: 18840

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 5835 AN: 11020

East Asian (EAS) AF: 0.687 AC: 14040 AN: 20430

South Asian (SAS) AF: 0.283 AC: 7829 AN: 27704

European-Finnish (FIN) AF: 0.432 AC: 12556 AN: 29068

Middle Eastern (MID) AF: 0.444 AC: 982 AN: 2212

European-Non Finnish (NFE) AF: 0.363 AC: 258699 AN: 712126

Other (OTH) AF: 0.389 AC: 12939 AN: 33234

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

African (AFR) AF: 0.250 AC: 10363 AN: 41508

American (AMR) AF: 0.460 AC: 7011 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1256 AN: 3464

East Asian (EAS) AF: 0.404 AC: 2091 AN: 5170

South Asian (SAS) AF: 0.189 AC: 910 AN: 4814

European-Finnish (FIN) AF: 0.312 AC: 3299 AN: 10590

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22226 AN: 67976

Other (OTH) AF: 0.333 AC: 701 AN: 2108

Alfa AF: 0.325 Hom.: 1068

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
PhyloP100		2.9

Splicing

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

Other links and lift over

dbSNP: rs561845; hg19: chr11-118558827;