rs17356414

Variant names:

• chr1-58853836-C-A
• rs17356414
• ENST00000419531.3:n.154-39709C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-58853836-C-A
• chr1-58853836-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000419531.3(JUN-DT):​n.154-39709C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
• Consequence: JUN-DT ENST00000419531.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.39
• Publications: 3 publications found

Genes affected

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

LOC107984961 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
JUN-DT	NR_034014.1	n.156-39709C>A		intron_variant	Intron 1 of 3
JUN-DT	NR_034015.1	n.156-39709C>A		intron_variant	Intron 1 of 2
JUN-DT	NR_108106.1	n.156-45211C>A		intron_variant	Intron 1 of 1
LOC107984961	XR_001738081.2	n.187+1705G>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
JUN-DT	ENST00000419531.3	n.154-39709C>A		intron_variant	Intron 1 of 3	4
JUN-DT	ENST00000649834.1	n.179-42421C>A		intron_variant	Intron 1 of 2
JUN-DT	ENST00000653297.1	n.179-32735C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 10908

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.040
DANN	Benign	0.55
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs17356414; hg19: chr1-59319508;