ENST00000780724.1:n.489A>G

Variant names:

• chr2-2333368-A-G
• rs17039584
• ENST00000780724.1:n.489A>G

Variant summary

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

The ENST00000780724.1(ENSG00000301667):​n.489A>G 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 0.114 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: ENSG00000301667 ENST00000780724.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.545
• Publications: 4 publications found

Genes affected

ENSG00000301667 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000780724.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301667	ENST00000780724.1		n.489A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000289941	ENST00000701928.2		n.-78T>C		upstream_gene	N/A

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

African (AFR) AF: 0.0290 AC: 1206 AN: 41544

American (AMR) AF: 0.131 AC: 2002 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3470

East Asian (EAS) AF: 0.345 AC: 1776 AN: 5150

South Asian (SAS) AF: 0.139 AC: 672 AN: 4822

European-Finnish (FIN) AF: 0.212 AC: 2243 AN: 10578

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8724 AN: 67950

Other (OTH) AF: 0.110 AC: 232 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	13
DANN	Benign	0.66
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs17039584; hg19: chr2-2337140;