chr1-58785425-T-G

Variant names:

• chr1-58785425-T-G
• rs2760501
• ENST00000419531.3:n.153+120T>G

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+120T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 450,380 control chromosomes in the GnomAD database, including 16,799 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 0.28 (12126 hom., cov: 29)
  • Exomes 𝑓: 0.13 (4673 hom.)
• Consequence: JUN-DT ENST00000419531.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250
• Publications: 10 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=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JUN-DT	NR_034014.1	n.155+120T>G		intron_variant	Intron 1 of 3
JUN-DT	NR_034015.1	n.155+120T>G		intron_variant	Intron 1 of 2
JUN-DT	NR_108106.1	n.155+120T>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JUN-DT	ENST00000419531.3	n.153+120T>G		intron_variant	Intron 1 of 3	4
JUN-DT	ENST00000649834.1	n.178+120T>G		intron_variant	Intron 1 of 2
JUN-DT	ENST00000653297.1	n.178+120T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.279 AC: 41721 AN: 149656 Hom.: 12072 Cov.: 29

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.0718

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.0958

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0746

Gnomad OTH AF: 0.239

GnomAD4 exome AF: 0.129 AC: 38731 AN: 300618 Hom.: 4673 AF XY: 0.129 AC XY: 22023 AN XY: 171332

African (AFR) AF: 0.753 AC: 6449 AN: 8564

American (AMR) AF: 0.166 AC: 4509 AN: 27094

Ashkenazi Jewish (ASJ) AF: 0.0661 AC: 691 AN: 10460

East Asian (EAS) AF: 0.157 AC: 1441 AN: 9186

South Asian (SAS) AF: 0.179 AC: 10611 AN: 59434

European-Finnish (FIN) AF: 0.0954 AC: 1169 AN: 12260

Middle Eastern (MID) AF: 0.145 AC: 299 AN: 2062

European-Non Finnish (NFE) AF: 0.0738 AC: 11623 AN: 157542

Other (OTH) AF: 0.138 AC: 1939 AN: 14016

GnomAD4 genome AF: 0.279 AC: 41831 AN: 149762 Hom.: 12126 Cov.: 29 AF XY: 0.277 AC XY: 20159 AN XY: 72810

African (AFR) AF: 0.742 AC: 30348 AN: 40896

American (AMR) AF: 0.189 AC: 2784 AN: 14748

Ashkenazi Jewish (ASJ) AF: 0.0718 AC: 247 AN: 3440

East Asian (EAS) AF: 0.162 AC: 806 AN: 4988

South Asian (SAS) AF: 0.215 AC: 1019 AN: 4738

European-Finnish (FIN) AF: 0.0958 AC: 959 AN: 10008

Middle Eastern (MID) AF: 0.162 AC: 47 AN: 290

European-Non Finnish (NFE) AF: 0.0745 AC: 5042 AN: 67652

Other (OTH) AF: 0.240 AC: 503 AN: 2092

Alfa AF: 0.148 Hom.: 12499

Bravo AF: 0.304

Asia WGS AF: 0.232 AC: 805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	13
DANN	Benign	0.82
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs2760501; hg19: chr1-59251097; COSMIC: COSV107467629;