1-58859954-T-C

Variant names:

• chr1-58859954-T-C
• rs4601609
• ENST00000419531.3:n.154-33591T>C

Variant summary

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

The ENST00000419531.3(JUN-DT):​n.154-33591T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0599 in 152,290 control chromosomes in the GnomAD database, including 373 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 0.060 (373 hom., cov: 32)
• Consequence: JUN-DT ENST00000419531.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.130
• Publications: 5 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JUN-DT	NR_034014.1	n.156-33591T>C		intron_variant	Intron 1 of 3
JUN-DT	NR_034015.1	n.156-33591T>C		intron_variant	Intron 1 of 2
JUN-DT	NR_108106.1	n.156-39093T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JUN-DT	ENST00000419531.3	n.154-33591T>C		intron_variant	Intron 1 of 3	4
JUN-DT	ENST00000649834.1	n.179-36303T>C		intron_variant	Intron 1 of 2
JUN-DT	ENST00000653297.1	n.179-26617T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0598 AC: 9105 AN: 152172 Hom.: 370 Cov.: 32

Gnomad AFR AF: 0.0889

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0829

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.0602

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0250

Gnomad OTH AF: 0.0492

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

GnomAD4 genome AF: 0.0599 AC: 9120 AN: 152290 Hom.: 373 Cov.: 32 AF XY: 0.0638 AC XY: 4749 AN XY: 74466

African (AFR) AF: 0.0887 AC: 3687 AN: 41558

American (AMR) AF: 0.0837 AC: 1281 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0202 AC: 70 AN: 3472

East Asian (EAS) AF: 0.158 AC: 817 AN: 5182

South Asian (SAS) AF: 0.0601 AC: 290 AN: 4828

European-Finnish (FIN) AF: 0.106 AC: 1120 AN: 10612

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0250 AC: 1699 AN: 68018

Other (OTH) AF: 0.0482 AC: 102 AN: 2116

Alfa AF: 0.0362 Hom.: 733

Bravo AF: 0.0592

Asia WGS AF: 0.124 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.64
DANN	Benign	0.63
PhyloP100		0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs4601609; hg19: chr1-59325626;