1-58891154-T-C

Variant names:

• chr1-58891154-T-C
• rs6661505
• ENST00000419531.3:n.154-2391T>C

Variant summary

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

The ENST00000634763.1(LINC02777):​n.346-1946A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,936 control chromosomes in the GnomAD database, including 8,728 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 0.33 (8728 hom., cov: 31)
• Consequence: LINC02777 ENST00000634763.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102
• Publications: 6 publications found

Genes affected

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

LINC02777 (HGNC:54297): (long intergenic non-protein coding RNA 2777)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634763.1. 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.156-2391T>C		intron	N/A
	JUN-DT	NR_034015.1		n.156-2391T>C		intron	N/A
	JUN-DT	NR_108106.1		n.156-7893T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	JUN-DT	ENST00000419531.3	TSL:4	n.154-2391T>C		intron	N/A
	LINC02777	ENST00000423408.6	TSL:5	n.406-1946A>G		intron	N/A
	LINC02777	ENST00000427292.2	TSL:3	n.406+4691A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50448 AN: 151818 Hom.: 8729 Cov.: 31

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.332 AC: 50465 AN: 151936 Hom.: 8728 Cov.: 31 AF XY: 0.335 AC XY: 24914 AN XY: 74276

African (AFR) AF: 0.295 AC: 12206 AN: 41394

American (AMR) AF: 0.399 AC: 6091 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1216 AN: 3470

East Asian (EAS) AF: 0.495 AC: 2553 AN: 5162

South Asian (SAS) AF: 0.503 AC: 2423 AN: 4818

European-Finnish (FIN) AF: 0.272 AC: 2879 AN: 10572

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21940 AN: 67934

Other (OTH) AF: 0.357 AC: 753 AN: 2108

Alfa AF: 0.339 Hom.: 7958

Bravo AF: 0.342

Asia WGS AF: 0.468 AC: 1626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.86
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs6661505; hg19: chr1-59356826;