1-58835546-T-C

Variant names:

• chr1-58835546-T-C
• rs1815274
• ENST00000419531.3:n.153+50241T>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.153+50241T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 152,050 control chromosomes in the GnomAD database, including 20,783 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 0.49 (20783 hom., cov: 32)
• Consequence: JUN-DT ENST00000419531.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710
• Publications: 1 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 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.155+50241T>C		intron	N/A
	JUN-DT	NR_034015.1		n.155+50241T>C		intron	N/A
	JUN-DT	NR_108106.1		n.155+50241T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JUN-DT	ENST00000419531.3	TSL:4	n.153+50241T>C		intron	N/A
	JUN-DT	ENST00000649834.1		n.178+50241T>C		intron	N/A
	JUN-DT	ENST00000653297.1		n.178+50241T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74549 AN: 151930 Hom.: 20784 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.490 AC: 74553 AN: 152050 Hom.: 20783 Cov.: 32 AF XY: 0.497 AC XY: 36943 AN XY: 74316

African (AFR) AF: 0.207 AC: 8581 AN: 41476

American (AMR) AF: 0.525 AC: 8023 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2065 AN: 3472

East Asian (EAS) AF: 0.630 AC: 3251 AN: 5164

South Asian (SAS) AF: 0.514 AC: 2478 AN: 4822

European-Finnish (FIN) AF: 0.706 AC: 7462 AN: 10574

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40835 AN: 67948

Other (OTH) AF: 0.517 AC: 1090 AN: 2110

Alfa AF: 0.565 Hom.: 94309

Bravo AF: 0.467

Asia WGS AF: 0.534 AC: 1856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.8
DANN	Benign	0.50
PhyloP100		-0.071

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: rs1815274;

hg19: chr1-59301218;