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 ENST00000757145.1(LINC02798):​n.1049A>G variant causes a non coding transcript exon 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 ENST00000757145.1 non_coding_transcript_exon
• 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757145.1. 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
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.1066-30671A>G		intron	N/A
	LINC02798	ENST00000757145.1		n.1049A>G		non_coding_transcript_exon	Exon 3 of 3
	LINC02798	ENST00000650414.1		n.595+1284A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4844616;

hg19: chr1-121171208;

COSMIC: COSV69885480;