ENST00000417218.2:n.1066-1382G>T

Variant names:

• chr1-121458637-G-T
• rs6600671
• ENST00000417218.2:n.1066-1382G>T

Variant summary

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

The ENST00000417218.2(LINC02798):​n.1066-1382G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 151,964 control chromosomes in the GnomAD database, including 29,694 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 0.62 (29694 hom., cov: 32)
• Consequence: LINC02798 ENST00000417218.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.131
• Publications: 23 publications found

Genes affected

LINC02798 (HGNC:54323): (long intergenic non-protein coding RNA 2798)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417218.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02798	ENST00000417218.2	TSL:1	n.1066-1382G>T		intron	N/A
	LINC02798	ENST00000650414.1		n.596-1382G>T		intron	N/A
	LINC02798	ENST00000664311.1		n.330-1382G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.624 AC: 94689 AN: 151846 Hom.: 29663 Cov.: 32

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.624 AC: 94786 AN: 151964 Hom.: 29694 Cov.: 32 AF XY: 0.626 AC XY: 46460 AN XY: 74250

African (AFR) AF: 0.648 AC: 26874 AN: 41478

American (AMR) AF: 0.621 AC: 9460 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1890 AN: 3464

East Asian (EAS) AF: 0.809 AC: 4180 AN: 5168

South Asian (SAS) AF: 0.491 AC: 2364 AN: 4818

European-Finnish (FIN) AF: 0.659 AC: 6967 AN: 10572

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 41112 AN: 67920

Other (OTH) AF: 0.620 AC: 1307 AN: 2108

Alfa AF: 0.614 Hom.: 56584

Bravo AF: 0.631

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.67
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs6600671; hg19: chr1-121200490;