1-58788023-T-C

Variant names:

• chr1-58788023-T-C
• rs2984915
• ENST00000419531.3:n.153+2718T>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+2718T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 152,206 control chromosomes in the GnomAD database, including 48,663 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 0.76 (48663 hom., cov: 32)
• Consequence: JUN-DT ENST00000419531.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.924 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.155+2718T>C		intron	N/A
	JUN-DT	NR_034015.1		n.155+2718T>C		intron	N/A
	JUN-DT	NR_108106.1		n.155+2718T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JUN-DT	ENST00000419531.3	TSL:4	n.153+2718T>C		intron	N/A
	JUN-DT	ENST00000649834.1		n.178+2718T>C		intron	N/A
	JUN-DT	ENST00000653297.1		n.178+2718T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.760 AC: 115619 AN: 152088 Hom.: 48657 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.945

Gnomad EAS AF: 0.848

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.928

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.760 AC: 115636 AN: 152206 Hom.: 48663 Cov.: 32 AF XY: 0.762 AC XY: 56676 AN XY: 74416

African (AFR) AF: 0.361 AC: 14974 AN: 41462

American (AMR) AF: 0.870 AC: 13314 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.945 AC: 3282 AN: 3472

East Asian (EAS) AF: 0.848 AC: 4396 AN: 5184

South Asian (SAS) AF: 0.790 AC: 3811 AN: 4826

European-Finnish (FIN) AF: 0.928 AC: 9837 AN: 10604

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.930 AC: 63255 AN: 68030

Other (OTH) AF: 0.796 AC: 1681 AN: 2112

Alfa AF: 0.863 Hom.: 156789

Bravo AF: 0.741

Asia WGS AF: 0.782 AC: 2721 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	7.4
DANN	Benign	0.52
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs2984915; hg19: chr1-59253695;