rs7552624

Variant names:

• chr1-58847764-T-C
• rs7552624
• ENST00000419531.3:n.154-45781T>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.154-45781T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,128 control chromosomes in the GnomAD database, including 4,753 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 0.23 (4753 hom., cov: 32)
• Consequence: JUN-DT ENST00000419531.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.916
• Publications: 0 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 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.156-45781T>C		intron	N/A
	JUN-DT	NR_034015.1		n.156-45781T>C		intron	N/A
	JUN-DT	NR_108106.1		n.156-51283T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JUN-DT	ENST00000419531.3	TSL:4	n.154-45781T>C		intron	N/A
	ENSG00000231740	ENST00000424592.1	TSL:3	n.31+3460A>G		intron	N/A
	JUN-DT	ENST00000649834.1		n.179-48493T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35378 AN: 152010 Hom.: 4752 Cov.: 32

Gnomad AFR AF: 0.0929

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.233 AC: 35390 AN: 152128 Hom.: 4753 Cov.: 32 AF XY: 0.239 AC XY: 17769 AN XY: 74368

African (AFR) AF: 0.0927 AC: 3851 AN: 41522

American (AMR) AF: 0.248 AC: 3784 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 990 AN: 3468

East Asian (EAS) AF: 0.374 AC: 1936 AN: 5170

South Asian (SAS) AF: 0.338 AC: 1632 AN: 4822

European-Finnish (FIN) AF: 0.314 AC: 3326 AN: 10582

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18850 AN: 67968

Other (OTH) AF: 0.254 AC: 537 AN: 2114

Alfa AF: 0.251 Hom.: 2003

Bravo AF: 0.225

Asia WGS AF: 0.334 AC: 1161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.18
DANN	Benign	0.39
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs7552624; hg19: chr1-59313436;