3-120866468-C-T

Variant names:

• chr3-120866468-C-T
• rs322458
• ENST00000655299.1:n.429+1801G>A

Variant summary

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

The ENST00000655299.1(LINC02049):​n.429+1801G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,946 control chromosomes in the GnomAD database, including 11,546 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 0.39 (11546 hom., cov: 32)
• Consequence: LINC02049 ENST00000655299.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.661
• Publications: 9 publications found

Genes affected

LINC02049 (HGNC:52889): (long intergenic non-protein coding RNA 2049)

ENSG00000287366 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655299.1. 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
	LINC02049	ENST00000655299.1		n.429+1801G>A		intron	N/A
	ENSG00000287366	ENST00000658056.1		n.432-5224C>T		intron	N/A
	LINC02049	ENST00000661060.1		n.912+1801G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58670 AN: 151828 Hom.: 11543 Cov.: 32

Gnomad AFR AF: 0.451

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.386 AC: 58702 AN: 151946 Hom.: 11546 Cov.: 32 AF XY: 0.378 AC XY: 28094 AN XY: 74240

African (AFR) AF: 0.450 AC: 18657 AN: 41430

American (AMR) AF: 0.370 AC: 5646 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1498 AN: 3468

East Asian (EAS) AF: 0.198 AC: 1020 AN: 5160

South Asian (SAS) AF: 0.277 AC: 1334 AN: 4822

European-Finnish (FIN) AF: 0.334 AC: 3532 AN: 10566

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25873 AN: 67932

Other (OTH) AF: 0.381 AC: 804 AN: 2112

Alfa AF: 0.384 Hom.: 42255

Bravo AF: 0.393

Asia WGS AF: 0.218 AC: 759 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.36
DANN	Benign	0.52
PhyloP100		-0.66

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: rs322458;

hg19: chr3-120585315;