1-59053946-T-G

Variant names:

• chr1-59053946-T-G
• rs4598514
• ENST00000715609.1:n.346-78401T>G

Variant summary

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

The ENST00000715609.1(JUN-DT):​n.346-78401T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,210 control chromosomes in the GnomAD database, including 4,941 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 0.25 (4941 hom., cov: 33)
• Consequence: JUN-DT ENST00000715609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152
• Publications: 0 publications found

Genes affected

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

ENSG00000241042 (HGNC:):

LINC01358 (HGNC:50589): (long intergenic non-protein coding RNA 1358)

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 (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715609.1. 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
	LINC01358	NR_110626.2		n.238+32369T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JUN-DT	ENST00000715609.1		n.346-78401T>G		intron	N/A
	JUN-DT	ENST00000715610.1		n.1883-2745T>G		intron	N/A
	JUN-DT	ENST00000715611.1		n.177-34069T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37428 AN: 152092 Hom.: 4931 Cov.: 33

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.0977

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.246 AC: 37460 AN: 152210 Hom.: 4941 Cov.: 33 AF XY: 0.240 AC XY: 17901 AN XY: 74450

African (AFR) AF: 0.316 AC: 13103 AN: 41520

American (AMR) AF: 0.202 AC: 3097 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1023 AN: 3468

East Asian (EAS) AF: 0.0976 AC: 506 AN: 5186

South Asian (SAS) AF: 0.263 AC: 1267 AN: 4824

European-Finnish (FIN) AF: 0.194 AC: 2055 AN: 10602

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15407 AN: 67996

Other (OTH) AF: 0.254 AC: 536 AN: 2112

Alfa AF: 0.239 Hom.: 663

Bravo AF: 0.250

Asia WGS AF: 0.187 AC: 651 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	0.67
DANN	Benign	0.78
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs4598514; hg19: chr1-59519618;