rs73001406

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000789004.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302703	ENST00000789004.1		n.169G>A		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000302721	ENST00000789212.1		n.124C>T		non_coding_transcript_exon	Exon 1 of 2
	TREHP1	ENST00000531328.2	TSL:6	n.216-23C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs73001406;

hg19: chr11-118560857;