rs2999131

Variant names:

• chr1-58832146-G-C
• rs2999131
• ENST00000419531.3:n.153+46841G>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+46841G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,092 control chromosomes in the GnomAD database, including 14,093 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 0.41 (14093 hom., cov: 32)
• Consequence: JUN-DT ENST00000419531.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.882
• Publications: 0 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.613 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+46841G>C		intron	N/A
	JUN-DT	NR_034015.1		n.155+46841G>C		intron	N/A
	JUN-DT	NR_108106.1		n.155+46841G>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+46841G>C		intron	N/A
	JUN-DT	ENST00000649834.1		n.178+46841G>C		intron	N/A
	JUN-DT	ENST00000653297.1		n.178+46841G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61873 AN: 151972 Hom.: 14062 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.407 AC: 61964 AN: 152092 Hom.: 14093 Cov.: 32 AF XY: 0.399 AC XY: 29659 AN XY: 74336

African (AFR) AF: 0.619 AC: 25665 AN: 41470

American (AMR) AF: 0.411 AC: 6276 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1220 AN: 3468

East Asian (EAS) AF: 0.222 AC: 1151 AN: 5182

South Asian (SAS) AF: 0.282 AC: 1362 AN: 4822

European-Finnish (FIN) AF: 0.224 AC: 2367 AN: 10572

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22764 AN: 67994

Other (OTH) AF: 0.388 AC: 818 AN: 2108

Alfa AF: 0.373 Hom.: 1462

Bravo AF: 0.430

Asia WGS AF: 0.293 AC: 1024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.39
PhyloP100		-0.88

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: rs2999131;

hg19: chr1-59297818;