1-121429348-A-G

Position:

• chr1-121429348-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047438024.1(LINC02798):​c.*378-30671A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 151,998 control chromosomes in the GnomAD database, including 20,560 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 0.50 (20559 hom., cov: 31)
  • Exomes 𝑓: 0.63 (1 hom.)
• Consequence: LINC02798 XM_047438024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560

Genes affected

LINC02798 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02798	XM_047438024.1	c.*378-30671A>G		intron_variant			XP_047293980.1
LINC02798	XR_007066533.1	n.1275A>G		non_coding_transcript_exon_variant	3/3
LINC02798	XR_007066532.1	n.825+1284A>G		intron_variant
LINC02798	XR_007066534.1	n.550-30671A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02798	ENST00000417218.1	n.552-30671A>G		intron_variant		1
LINC02798	ENST00000650414.1	n.595+1284A>G		intron_variant
LINC02798	ENST00000664311.1	n.330-30671A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76603 AN: 151872 Hom.: 20552 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.530

GnomAD4 exome AF: 0.625 AC: 5 AN: 8 Hom.: 1 AF XY: 0.667 AC XY: 4 AN XY: 6

Gnomad4 AMR exome AF: 0.500

Gnomad4 NFE exome AF: 0.667

GnomAD4 genome AF: 0.504 AC: 76641 AN: 151990 Hom.: 20559 Cov.: 31 AF XY: 0.506 AC XY: 37561 AN XY: 74300

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.630

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.528

Alfa AF: 0.580 Hom.: 37950

Bravo AF: 0.495

Asia WGS AF: 0.466 AC: 1621 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4844616; hg19: chr1-121171208; COSMIC: COSV69885480;