1-121429348-A-G

Variant names:

• chr1-121429348-A-G
• rs4844616
• ENST00000417218.2:n.1066-30671A>G

Variant summary

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

The ENST00000417218.2(LINC02798):​n.1066-30671A>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 ENST00000417218.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560
• Publications: 14 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=-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 rank	MANE	Protein	UniProt
LINC02798	XR_007066533.1	n.1275A>G		non_coding_transcript_exon_variant	Exon 3 of 3
LINC02798	XM_047438024.1	c.*378-30671A>G		intron_variant	Intron 1 of 1		XP_047293980.1
LINC02798	XR_007066532.1	n.825+1284A>G		intron_variant	Intron 2 of 2
LINC02798	XR_007066534.1	n.550-30671A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02798	ENST00000417218.2	n.1066-30671A>G		intron_variant	Intron 1 of 1	1
LINC02798	ENST00000757145.1	n.1049A>G		non_coding_transcript_exon_variant	Exon 3 of 3
LINC02798	ENST00000650414.1	n.595+1284A>G		intron_variant	Intron 3 of 3

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

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.667 AC: 4 AN: 6

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.300 AC: 12449 AN: 41428

American (AMR) AF: 0.531 AC: 8114 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1824 AN: 3466

East Asian (EAS) AF: 0.630 AC: 3249 AN: 5156

South Asian (SAS) AF: 0.401 AC: 1934 AN: 4828

European-Finnish (FIN) AF: 0.644 AC: 6800 AN: 10556

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40542 AN: 67966

Other (OTH) AF: 0.528 AC: 1113 AN: 2108

Alfa AF: 0.559 Hom.: 62691

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
PhyloP100		0.056

Splicing

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

Other links and lift over

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