chr11-118690148-G-A

Variant names:

• chr11-118690148-G-A
• rs73001406
• ENST00000789004.1:n.169G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000789004.1(ENSG00000302703):​n.169G>A 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 0.227 in 473,236 control chromosomes in the GnomAD database, including 13,122 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 0.21 (3396 hom., cov: 32)
  • Exomes 𝑓: 0.24 (9726 hom.)
• Consequence: ENSG00000302703 ENST00000789004.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.678
• Publications: 24 publications found

Genes affected

ENSG00000302703 (HGNC:):

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TREHP1		n.118690148G>A		intragenic_variant
LOC105369519	XR_007062909.1	n.87+513G>A		intron_variant	Intron 1 of 3
LOC105369519	XR_007062910.1	n.-202G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302703	ENST00000789004.1	n.169G>A		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000302721	ENST00000789212.1	n.124C>T		non_coding_transcript_exon_variant	Exon 1 of 2
TREHP1	ENST00000531328.2	n.216-23C>T		intron_variant	Intron 1 of 3	6

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31267 AN: 152090 Hom.: 3389 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.198

GnomAD4 exome AF: 0.237 AC: 76219 AN: 321028 Hom.: 9726 Cov.: 3 AF XY: 0.245 AC XY: 41702 AN XY: 169916

African (AFR) AF: 0.134 AC: 1215 AN: 9042

American (AMR) AF: 0.188 AC: 2443 AN: 13016

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 1874 AN: 9410

East Asian (EAS) AF: 0.251 AC: 4567 AN: 18172

South Asian (SAS) AF: 0.336 AC: 13088 AN: 38982

European-Finnish (FIN) AF: 0.231 AC: 5310 AN: 22958

Middle Eastern (MID) AF: 0.218 AC: 346 AN: 1588

European-Non Finnish (NFE) AF: 0.228 AC: 43265 AN: 189674

Other (OTH) AF: 0.226 AC: 4111 AN: 18186

GnomAD4 genome AF: 0.206 AC: 31293 AN: 152208 Hom.: 3396 Cov.: 32 AF XY: 0.208 AC XY: 15489 AN XY: 74408

African (AFR) AF: 0.135 AC: 5623 AN: 41556

American (AMR) AF: 0.207 AC: 3160 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 696 AN: 3472

East Asian (EAS) AF: 0.268 AC: 1387 AN: 5174

South Asian (SAS) AF: 0.355 AC: 1709 AN: 4818

European-Finnish (FIN) AF: 0.227 AC: 2406 AN: 10584

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15669 AN: 67998

Other (OTH) AF: 0.199 AC: 421 AN: 2112

Alfa AF: 0.214 Hom.: 1074

Bravo AF: 0.195

Asia WGS AF: 0.280 AC: 972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.97
DANN	Benign	0.84
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs73001406; hg19: chr11-118560857;