ENST00000701928.1:n.-110T>C

Variant names:

• chr2-2333368-A-G
• rs17039584
• ENST00000701928.1:n.-110T>C

Variant summary

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

The ENST00000701928.1(ENSG00000289941):​n.-110T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,112 control chromosomes in the GnomAD database, including 1,360 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 0.11 (1360 hom., cov: 32)
• Consequence: ENSG00000289941 ENST00000701928.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.545

Genes affected

ENSG00000289941 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289941	ENST00000701928.1	n.-110T>C		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17376 AN: 151994 Hom.: 1353 Cov.: 32

Gnomad AFR AF: 0.0291

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.110

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.114 AC: 17386 AN: 152112 Hom.: 1360 Cov.: 32 AF XY: 0.120 AC XY: 8900 AN XY: 74334

Gnomad4 AFR AF: 0.0290

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.110

Alfa AF: 0.117 Hom.: 277

Bravo AF: 0.106

Asia WGS AF: 0.214 AC: 744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	13
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17039584; hg19: chr2-2337140;