rs11711889

chr3-153652877-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_146713.1(LINC02006):n.160+19298C>T variant causes a intron, non coding transcript 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 NR_146713.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02006	NR_146713.1	n.160+19298C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02006	ENST00000493214.2	n.160+19298C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0308

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.126

Alfa AF: 0.148 Hom.: 3045

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11711889; hg19: chr3-153370666;