3-153652877-G-A

Variant names:

• chr3-153652877-G-A
• rs11711889
• ENST00000493214.2:n.160+19298C>T

Variant summary

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

The ENST00000493214.2(LINC02006):​n.160+19298C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,216 control chromosomes in the GnomAD database, including 1,423 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 0.12 (1423 hom., cov: 33)
• Consequence: LINC02006 ENST00000493214.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314
• Publications: 4 publications found

Genes affected

LINC02006 (HGNC:52842): (long intergenic non-protein coding RNA 2006)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02006	NR_146713.1	n.160+19298C>T		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02006	ENST00000493214.2	n.160+19298C>T		intron_variant	Intron 3 of 6	2

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18129 AN: 152098 Hom.: 1421 Cov.: 33

Gnomad AFR AF: 0.0309

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.119 AC: 18136 AN: 152216 Hom.: 1423 Cov.: 33 AF XY: 0.124 AC XY: 9198 AN XY: 74414

African (AFR) AF: 0.0308 AC: 1282 AN: 41562

American (AMR) AF: 0.109 AC: 1666 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 552 AN: 3470

East Asian (EAS) AF: 0.245 AC: 1268 AN: 5178

South Asian (SAS) AF: 0.141 AC: 680 AN: 4830

European-Finnish (FIN) AF: 0.196 AC: 2072 AN: 10578

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10290 AN: 68000

Other (OTH) AF: 0.126 AC: 267 AN: 2112

Alfa AF: 0.140 Hom.: 4558

Bravo AF: 0.109

Asia WGS AF: 0.160 AC: 554 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.90
DANN	Benign	0.38
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs11711889; hg19: chr3-153370666;