rs16831763

Variant names:

• chr3-120826130-A-G
• rs16831763
• ENST00000661060.1:n.947-13442T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000661060.1(LINC02049):​n.947-13442T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0306 in 152,300 control chromosomes in the GnomAD database, including 303 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 0.031 (303 hom., cov: 32)
• Consequence: LINC02049 ENST00000661060.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.23).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661060.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02049	NR_135570.1		n.89+10139T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02049	ENST00000661060.1		n.947-13442T>C		intron	N/A
	LINC02049	ENST00000720436.1		n.290-13442T>C		intron	N/A
	LINC02049	ENST00000720437.1		n.359-13442T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0305 AC: 4641 AN: 152182 Hom.: 296 Cov.: 32

Gnomad AFR AF: 0.00606

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.0536

Gnomad SAS AF: 0.0773

Gnomad FIN AF: 0.0385

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0107

Gnomad OTH AF: 0.0272

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

GnomAD4 genome AF: 0.0306 AC: 4655 AN: 152300 Hom.: 303 Cov.: 32 AF XY: 0.0356 AC XY: 2649 AN XY: 74468

African (AFR) AF: 0.00606 AC: 252 AN: 41570

American (AMR) AF: 0.162 AC: 2479 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0118 AC: 41 AN: 3472

East Asian (EAS) AF: 0.0538 AC: 278 AN: 5172

South Asian (SAS) AF: 0.0769 AC: 371 AN: 4824

European-Finnish (FIN) AF: 0.0385 AC: 409 AN: 10616

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0107 AC: 727 AN: 68038

Other (OTH) AF: 0.0265 AC: 56 AN: 2116

Alfa AF: 0.0182 Hom.: 191

Bravo AF: 0.0375

Asia WGS AF: 0.0790 AC: 273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.23
CADD	Benign	17
DANN	Benign	0.82
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs16831763; hg19: chr3-120544977;