rs4646999

Variant names:

• chr1-58784780-A-G
• rs4646999
• ENST00000685887.2:n.525A>G

Variant summary

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

The ENST00000685887.2(JUN-DT):​n.525A>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 0.566 in 151,880 control chromosomes in the GnomAD database, including 25,605 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 0.57 (25605 hom., cov: 31)
• Consequence: JUN-DT ENST00000685887.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180
• Publications: 7 publications found

Genes affected

JUN-DT (HGNC:49450): (JUN divergent transcript)

ENSG00000290013 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000685887.2. 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
	JUN-DT	ENST00000685887.2		n.525A>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000290013	ENST00000702469.1		n.156T>C		non_coding_transcript_exon	Exon 1 of 1
	JUN-DT	ENST00000842960.1		n.64+551A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85917 AN: 151758 Hom.: 25588 Cov.: 31

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.566 AC: 85965 AN: 151880 Hom.: 25605 Cov.: 31 AF XY: 0.573 AC XY: 42508 AN XY: 74216

African (AFR) AF: 0.358 AC: 14835 AN: 41396

American (AMR) AF: 0.663 AC: 10141 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2078 AN: 3470

East Asian (EAS) AF: 0.625 AC: 3199 AN: 5116

South Asian (SAS) AF: 0.606 AC: 2906 AN: 4798

European-Finnish (FIN) AF: 0.715 AC: 7563 AN: 10572

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.638 AC: 43347 AN: 67920

Other (OTH) AF: 0.555 AC: 1170 AN: 2108

Alfa AF: 0.613 Hom.: 43941

Bravo AF: 0.553

Asia WGS AF: 0.608 AC: 2117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.9
DANN	Benign	0.69
PhyloP100		0.018

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: rs4646999;

hg19: chr1-59250452;