chr1-59006725-A-C

Variant names:

• chr1-59006725-A-C
• rs2716140
• ENST00000715609.1:n.345+52806A>C

Variant summary

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

The ENST00000715609.1(JUN-DT):​n.345+52806A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 152,024 control chromosomes in the GnomAD database, including 14,879 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 0.44 (14879 hom., cov: 32)
• Consequence: JUN-DT ENST00000715609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• Publications: 10 publications found

Genes affected

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

ENSG00000241042 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715609.1. 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
	JUN-DT	ENST00000715609.1		n.345+52806A>C		intron	N/A
	JUN-DT	ENST00000715610.1		n.397-13770A>C		intron	N/A
	JUN-DT	ENST00000715611.1		n.176+52806A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66104 AN: 151906 Hom.: 14868 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.435 AC: 66151 AN: 152024 Hom.: 14879 Cov.: 32 AF XY: 0.431 AC XY: 31999 AN XY: 74300

African (AFR) AF: 0.546 AC: 22622 AN: 41460

American (AMR) AF: 0.379 AC: 5795 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1549 AN: 3466

East Asian (EAS) AF: 0.200 AC: 1034 AN: 5174

South Asian (SAS) AF: 0.317 AC: 1528 AN: 4814

European-Finnish (FIN) AF: 0.431 AC: 4546 AN: 10544

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27645 AN: 67964

Other (OTH) AF: 0.445 AC: 940 AN: 2114

Alfa AF: 0.411 Hom.: 22517

Bravo AF: 0.433

Asia WGS AF: 0.268 AC: 931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.4
DANN	Benign	0.57
PhyloP100		-0.30

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: rs2716140;

hg19: chr1-59472397;