1-58853836-C-T

Variant names:

• chr1-58853836-C-T
• rs17356414
• ENST00000419531.3:n.154-39709C>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.154-39709C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 151,882 control chromosomes in the GnomAD database, including 5,597 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 0.26 (5597 hom., cov: 30)
• Consequence: JUN-DT ENST00000419531.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.39
• Publications: 3 publications found

Genes affected

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

LOC107984961 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.331 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JUN-DT	NR_034014.1		n.156-39709C>T		intron	N/A
	JUN-DT	NR_034015.1		n.156-39709C>T		intron	N/A
	JUN-DT	NR_108106.1		n.156-45211C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JUN-DT	ENST00000419531.3	TSL:4	n.154-39709C>T		intron	N/A
	JUN-DT	ENST00000649834.1		n.179-42421C>T		intron	N/A
	JUN-DT	ENST00000653297.1		n.179-32735C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38817 AN: 151764 Hom.: 5595 Cov.: 30

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.256 AC: 38822 AN: 151882 Hom.: 5597 Cov.: 30 AF XY: 0.251 AC XY: 18641 AN XY: 74218

African (AFR) AF: 0.115 AC: 4774 AN: 41434

American (AMR) AF: 0.293 AC: 4475 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1023 AN: 3468

East Asian (EAS) AF: 0.195 AC: 1006 AN: 5170

South Asian (SAS) AF: 0.241 AC: 1159 AN: 4814

European-Finnish (FIN) AF: 0.265 AC: 2785 AN: 10510

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.335 AC: 22741 AN: 67926

Other (OTH) AF: 0.251 AC: 527 AN: 2102

Alfa AF: 0.294 Hom.: 10908

Bravo AF: 0.256

Asia WGS AF: 0.216 AC: 753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.070
DANN	Benign	0.53
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs17356414; hg19: chr1-59319508;