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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374069	XR_924398.4	n.912+1801G>A		intron_variant	Intron 4 of 5
LOC105374069	XR_924399.4	n.429+1801G>A		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02049	ENST00000655299.1	n.429+1801G>A		intron_variant	Intron 4 of 5
ENSG00000287366	ENST00000658056.1	n.432-5224C>T		intron_variant	Intron 4 of 4
LINC02049	ENST00000661060.1	n.912+1801G>A		intron_variant	Intron 4 of 5

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 v4.3

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

Other links and lift over

dbSNP: rs322458; hg19: chr3-120585315;