1-58849530-A-T

Variant names:

• chr1-58849530-A-T
• rs1853432
• ENST00000419531.3:n.154-44015A>T

Variant summary

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

The ENST00000419531.3(JUN-DT):​n.154-44015A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.753 in 152,248 control chromosomes in the GnomAD database, including 43,484 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 0.75 (43484 hom., cov: 33)
• Consequence: JUN-DT ENST00000419531.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 1 publications found

Genes affected

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

ENSG00000231740 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419531.3. 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
	JUN-DT	NR_034014.1		n.156-44015A>T		intron	N/A
	JUN-DT	NR_034015.1		n.156-44015A>T		intron	N/A
	JUN-DT	NR_108106.1		n.156-49517A>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JUN-DT	ENST00000419531.3	TSL:4	n.154-44015A>T		intron	N/A
	ENSG00000231740	ENST00000424592.1	TSL:3	n.31+1694T>A		intron	N/A
	JUN-DT	ENST00000649834.1		n.179-46727A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.753 AC: 114493 AN: 152130 Hom.: 43434 Cov.: 33

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.767

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.753 AC: 114598 AN: 152248 Hom.: 43484 Cov.: 33 AF XY: 0.745 AC XY: 55482 AN XY: 74442

African (AFR) AF: 0.801 AC: 33295 AN: 41548

American (AMR) AF: 0.693 AC: 10602 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2562 AN: 3470

East Asian (EAS) AF: 0.541 AC: 2801 AN: 5176

South Asian (SAS) AF: 0.491 AC: 2367 AN: 4822

European-Finnish (FIN) AF: 0.767 AC: 8129 AN: 10598

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.768 AC: 52257 AN: 68014

Other (OTH) AF: 0.754 AC: 1593 AN: 2112

Alfa AF: 0.766 Hom.: 5551

Bravo AF: 0.755

Asia WGS AF: 0.531 AC: 1844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.24
DANN	Benign	0.67
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs1853432; hg19: chr1-59315202;